Trimgalore github 4 and cutadapt 2. Is the effect data dependent in any way? Are certain files susceptible and others not? Is it possible to intercept the cutadapt command and just try running that independently? Could there be something which is causing Apr 13, 2022 · Would you recommend a much more stringent size threshold in TrimGalore (say, 100bp reads or even higher) to balance the libraries? I know this will likely reduce the yield substantially, but it might be worth the sacrifice. Basically, align two paired-end reads and trim the overhangs (which would be adapters). There is a polyA option in trim_galore that allows to trim off polyA at Jan 7, 2022 · Since TrimGalore uses the TruSeq adapter prefix as default and that since Illumina is rebranding to Illumina kits (which I'm assuming will use the different adapter CTGTCTCTTATACACATCT), will this cause issues for TrimGalore? or would the automatic adapter detection pick this up? Feb 16, 2024 · A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data - FelixKrueger/TrimGalore GitHub is where people build software. 4_dev: Trim sequences with trim-galore (Krueger, 2015). Nov 29, 2022 · However, I am unsure how to provide the --discard-trimmed , the changing -O and the --nextseq 10 option as they are executed in different rounds. /trim_galore --gzip --illumina SRR1508529. gz file during the run, Jun 11, 2020 · I am trying to understand the multi-core usage instructions. Best regards. I can see the t Jan 28, 2025 · FelixKrueger / TrimGalore Public Notifications You must be signed in to change notification settings Fork 156 Star 531 Jul 26, 2020 · Hi, I ran the trimGalore on my paired end DNA seq. Feb 16, 2022 · TrimGalore: Error in FastQ fileUnanswered yaaminiv asked this question in Q&A TrimGalore: Error in FastQ file #1401 yaaminiv Feb 16, 2022 · 1 comment Return to top Trabajo de tesis de maestría. Ubuntu 18. More than 100 million people use GitHub to discover, fork, and contribute to over 420 million projects. Trim Galore is now also available from GitHub. I removed it manually and now it works just fine. Jan 15, 2024 · nextflow. md at master · Shicheng-Guo/TrimGalore-1 Jun 6, 2024 · Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. I'm still seeing high %A and %T per base sequence content that the beginning of my reads after removing Nextera adapters. It says for --cores 2 would actually use up to 9 cores (2 input, 2 output, 4 cutadapt, 1 trim galore). I have a pipeline that cuts automatically using trimgalore, however sometimes people send me data t Jun 13, 2023 · I am not proficient in removing adapters, as I have always relied on TrimGalore's automatic recognition before. 10 of cutadapt (I didn't realise we were using a development version, instead of the latest stable one), but I'll try to make some time to check whether your latest development version works fine with cutadapt's latest development version. Do you think this is because cutadapt Mar 7, 2019 · Hello I ran trim_galore using the following command line: . 5 to trim the adapter sequences from some paired-end WGS data that was prepared using Illumina's DNA PCR-Free prep, which uses adapter sequences CTGTCTCTTATACACATCT+ATG Mar 29, 2017 · A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data - TrimGalore-1/Docs/Trim_Galore_User_Guide. I was given the error shown as below: Jul 31, 2019 · When no adapter is found, trim galore defaults to the illumina sequence and tries to remove this. You are invited to leave comments, feature request or bug reports over there! A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data - Shicheng-Guo/TrimGalore-1 GitHub is where trimgalore builds software. You are invited to leave comments, feature request or bug reports over there! For MspI-digested RRBS libraries, Trim Galore! performs quality and adapter trimming in two subsequent steps. Dec 13, 2017 · Hi Tim, If you move to the folder containing the input files, you should be able to run e. A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data - FelixKrueger/TrimGalore Mar 26, 2025 · The output that you would have expected: All Read 1 sequences will be trimmed by 3 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 3 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Output file(s) will be GZIP compressed A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data - Community Standards · FelixKrueger/TrimGalore Jul 28, 2020 · Thanks for this excellent resource. More than 150 million people use GitHub to discover, fork, and contribute to over 420 million projects. Assuming that the data provided uses Sanger encoded Phre Mar 26, 2020 · Hi, I'm using TrimGalore 0. Jun 17, 2025 · A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data - panayiotis/trim_galore trim-galore Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control Homepage: https://github. Contribute to outcastaaa/bioinformatics-learning development by creating an account on GitHub. fq. gz was generated, then sample_1_val. Thank you also for the pigz suggestion, am testing it right now 👍 Oct 6, 2023 · Hi Felix, If you remember my email last week where I shared my fastqc and Trim_galore results with you. 04 with trim galore! Contribute to chrishah/trim_galore-docker development by creating an account on GitHub. Contribute to movingpictures83/TrimGalore development by creating an account on GitHub. com /FelixKrueger/ TrimGalore Mar 13, 2023 · The TrimGalore user guide is essential to understanding the application and making the most of it. # Run Trim Galore . Contribute to xiaotao-star/TrimGalore_Installation development by creating an account on GitHub. Tried --max_n 1 as well, but N reads with more than 1 N are not removed. version of tools are written below. The guide and this page should help you to get started with your simulations. I ran TrimGalore with the following command (which I Jan 17, 2020 · FelixKrueger / TrimGalore Public Notifications You must be signed in to change notification settings Fork 156 Star 527 Aug 29, 2018 · FelixKrueger / TrimGalore Public Notifications You must be signed in to change notification settings Fork 156 Star 528 Jul 1, 2019 · Hi ! In the interest of benchmarking a pipeline, I have recently been running the same exact same files several times over through trim_galore. gz uncompresses to dir named TrimGalore-0. This feature, however, cannot be used with trim_galore, as it enforces the adapter Mar 6, 2024 · FelixKrueger / TrimGalore Public Notifications You must be signed in to change notification settings Fork 156 Star 531 Mar 8, 2024 · Hi. The job continues to run, but the files have not been updated in a long time. Learn more about blocking users. gz but I keep getting the error: No quality encoding type selected. Pardon me for the inconvinience. While running STAR aligner tool on these trimmed files ended up with the error that fix your fastq files. g. Contribute to yukoyoshida/trimgalore development by creating an account on GitHub. Trim Galore is a a Perl wrapper around two tools: Cutadapt and FastQC. trimgalore. Does trim_galore support such trimming strategy? From my understanding of the code, in paired-end processing, both fastq input files could be processed parallelly, but they are currently sequential. Dec 6, 2016 · So far, the option --rrbs removes two additional base pairs from the 3' end of reads if adapter contamination was found, and this applies to both Read 1 and Read 2. I normally use the default settings and proceed, t Feb 24, 2017 · In the user guide, the Full list of options for Trim galore! documentation describes illumina's default adapter as GATCGGAAGAGC, which seems to be missing an initial 'A' in comparison to the defaul Dec 22, 2021 · FelixKrueger / TrimGalore Public Notifications You must be signed in to change notification settings Fork 156 Star 530 Apr 21, 2020 · Hi, I just ran trim_galore on a set of paired-end reads as a test. My kit manual is that 5'-AATGATACGGCGACCA Automate your workflow from idea to production GitHub Actions makes it easy to automate all your software workflows, now with world-class CI/CD. What happens when you set --cores Oct 5, 2018 · We're running TrimGalore on a bunch of paired Illumina WGBS samples, and were getting a few FASTQ files as output, when we were expecting one left and right trimmed read per sample. I'm finding strange per base sequence content at the final position (25 Jan 30, 2018 · Sorry just saw the closed issues with questions of multithreaded support - sorry for opening the new issue! Another thought I had was it might be possible to use GNU parallel to run multiple instances of trim_galore if you have many samples. gz. Read 2 however does not technica Feb 9, 2023 · Hmm, this is a good question. gz fq_data/N1_2. Can I trim just one read in paired-end reads and run bismark for alignment next? Is there any problem because the read lengths make different after trimming? I use this: trim_galore --stringency 3 SRR2988823_1. fastq. Umm I;m sorry for uploading such a same problem again. org/bioconda/trim-galore (b) direct install from GitHub # requires separate installation of Cutadapt and FastQC https:// github. My gut feeling would that if it manages to read from the input file and produces valid trimmed output files, it can't be so bad Maybe it would still be worth May 5, 2023 · Hello again, I wanted to ask a clarifying question about trimming multiple adapters from paired end reads. Regarding your interpretation of the methylation vs insert size correlation, we had guessed that was the case as well. Thank you for your help. I only became aware of this when I recently communicated with laboratory personnel. More than 94 million people use GitHub to discover, fork, and contribute to over 330 million projects. I generated a full trimmed. A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data - FelixKrueger/TrimGalore Trim Galore is now also available from GitHub. Proceeding with single-core trimm Apr 30, 2020 · Hi Felix, I'm working on a project that necessitates clipping 2x151nt reads down to 2x50nt. Since I re-downloaded the cutadapt, fastqc and TrimGalore again, multicore is not supported now. In both cases, the report s Mar 15, 2017 · FelixKrueger / TrimGalore Public Notifications You must be signed in to change notification settings Fork 150 Star 491 Trim-Galore! run freezes, but doesn't throw any errors! #202 Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Att Nov 26, 2019 · FelixKrueger / TrimGalore Public Notifications You must be signed in to change notification settings Fork 152 Star 495 Jul 10, 2019 · This is my first time using this software, and I went to know what do these output files mean? command: trim_galore --paired --phred33 --fastqc --gzip -o clean_fq fq_data/N1_1. I have successfully installed cutadapt version 3. I've just tried to run $ conda install trim-galore, (with bioconda included in my channels) and I encounter the following error: Found conflicts! Looking for inc Mar 20, 2019 · Hi, I am running in an issue with trim_galore version 0. for instance is it ok to put all options such as --illumina --rrbs --quality --three_prime_clip_R1 --clip_R2 in Hello, I am processing 150bp Illumina paired-end whole-exome sequenced tumor-normal sample pairs, with an ensemble of 6 somatic variant callers. To use, ensure that these two pieces of software are available and copy the trim_galore script to a location available on the PATH. Jan 28, 2020 · Hi Felix im wondering steps and order of options are important in Trim galore or not. Apr 16, 2023 · When I used trimgalore, the file sample_1_trimmed. md at master · FelixKrueger/TrimGalore Oct 13, 2023 · Overview & setting up In this session, we will run TrimGalore to filter our FASTQ files, removing: Any adapter sequences that are present in the reads Poor-quality bases at the start and end of the reads Reads that have become very short after the prior two steps For reference-based RNAseq, this step is sometimes considered optional, since current tools that align reads to the genome should A installation document for TrimGalore. However, in every run trim galore gets stuck on the trimming step and never goes to the next step. Oct 25, 2018 · Stop trimgalore from searching for adaptor #37 Closed djbradshaw2 opened this issue on Oct 25, 2018 · 5 comments Feb 5, 2021 · We ran TrimGalore, combined with FastQC arguments. Aug 29, 2018 · FelixKrueger / TrimGalore Public Notifications You must be signed in to change notification settings Fork 156 Star 528 Jul 1, 2019 · Hi ! In the interest of benchmarking a pipeline, I have recently been running the same exact same files several times over through trim_galore. When trim_galore reads the first line of cutadapt (around line num Oct 7, 2020 · Hi @FelixKrueger, thanks heaps for the quick response! I reverted back to version 2. Here is my command: /path/to/trim_galor Feb 22, 2019 · Failed to write to file issue - create output folder if it doesn't exist already #45 Aug 4, 2021 · I worked with TrimGalore as I was advised by the sequencing centre for trimming all Illumina adaptors when I asked for the primer set and it works amazingly well where I used the following code: tr Nov 20, 2020 · FelixKrueger / TrimGalore Public Notifications You must be signed in to change notification settings Fork 156 Star 530 Jun 21, 2018 · I am finding myself wanting to hard-trim reads to a certain length from the 5' end fairly often, and it should be straight forward to add a new option e. Jun 1, 2021 · First, thank you for using such a nice tool. Oct 31, 2016 · Problems or maybe bugs? #1 Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. When I trim the data with --rrbs and --non-directional, the CGA still remain at the beginning of reads. Jul 20, 2023 · Trim-galore not compatible with latest python inside docker container. After using Trim Galore to remove adapters, I encountered an issue with the FastQC report for R2 reads ac Oct 13, 2023 · Hey, I am trying to trim pacbio sequencing data in a fastq file using trim galore. Jan 30, 2017 · For this we have developed a wrapper script (trim_galore) that makes use of the publicly available adapter trimming tool Cutadapt and FastQC for optional quality control once the trimming process has completed. We have sequenced degraded FFPE samples and are seeing the TSO adapter at the start of read2 and in some reads poly-A t Nov 19, 2023 · Hello I am working with human whole-genome bisulfite sequencing data, and paired-end reads. For example: # Check that FastQC is installed . Also, s Feb 9, 2023 · Hmm, this is a good question. I have a problem setting TrimGalore. My command line is as follows: trim_galore --paired - Mar 14, 2019 · Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Is there a way to specify the base name for the output files. Feb 27, 2019 · Tried --max_n 0 to exclude reads with N, but there are still reads with Ns in the trimmed fastq. Contribute to BioDepot/TrimGalore development by creating an account on GitHub. com/FelixKrueger/TrimGalore May 18, 2018 · I have used TrimGalore on a recent dataset to fantastic results - thank yiu very much for creating such an effective and efficient tool! Can you please advise how to cite the software? FelixKrueger / TrimGalore Public Notifications You must be signed in to change notification settings Fork 156 Star 530 Feb 2, 2023 Jul 10, 2019 · In the Update TrimGalore User Guide md file, it states the following: "The auto-detection behaviour can be overruled by specifying an adapter sequence manually or by using --illumina, --nextera or --small_rna. Feb 19, 2019 · Apparantly the last line of my fastq file was empty and cutadapt couldn't cope with that. fastq I then get the following: Multicore support not enabled. gz 2_KC6141-WT_S112_R2_001. FastQC after trimming shows TruSeq adapter presence ( mostly starti Jun 28, 2024 · I m using TrimGalore to trim my BS-seq paired-end data, but there is an adapter just in one read (read 1). md at master · Shicheng-Guo/TrimGalore-1 FastQC issues with Java 11 #58 Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. fq Jul 22, 2020 · Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Install "Trim Galore" (a) using a conda environment conda install -c bioconda trim-galore https://anaconda. Oct 27, 2020 · When TrimGalore detects adapter sequence automatically, for example, there are some adapter lists by sequence platform (illumina, iontorrent, and so on). It ran correctly without issue. # Install Trim Galore . fasta" as adapter. Hello @FelixKrueger , Trim Galore seems to freeze at the adapter trimming step. Should I put them under the TrimGalore -a option? Or is there a workaround you could suggest? For the context: I would like to use cutadapt via TrimGalore because TrimGalore is integrated in the Nextflow RNA-seq pipeline. Howeve. gz irrespective of whether the current working directory contains spaces in its directory name, or am I mistaken? I suppose I could look into quoting file path names, but it seems that moving to the directory with the input files yourself, or chosing Mar 25, 2025 · Trim galore has run on tons of different systems - we've run it through multiple generations of our cluster, as well as on loads of cloud instance and we've never seen this. Análisis de metagenoma de Paragyromitra infula - Esmaland/An-lisis-Paragyromitra_infula GitHub is where people build software. I looked and found that the reads are not the same length in both the files. Mar 12, 2020 · Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. I have four species that have reads with a length of 251 and one species that has reads with a length of 151. fastq Is it necessary to use --paired option? Aug 2, 2023 · I have 150bp PE data from the non-directional rrbs library. gz file_R2. Aug 13, 2020 · FelixKrueger / TrimGalore Public Notifications You must be signed in to change notification settings Fork 156 Star 531 FelixKrueger / TrimGalore Public Notifications You must be signed in to change notification settings Fork 156 Star 518 Code Issues6 Pull requests Projects Security Jan 14, 2020 · Hi Felix, First, thank you very much for your prompt reply to my previous question on Bismark. Jul 28, 2021 · I have used Trim Galore v0. FelixKrueger / TrimGalore Public Notifications You must be signed in to change notification settings Fork 156 Star 532 Feb 19, 2020 · Thank you for your program! I'm coming across 2 issues. 6. gz and val_2. --hardtrim <INT> to accomplish this. Jul 27, 2021 · I am trying to trim WGBS data using TrimGalore but I observed that it is unable to trim all occurrences of the Illumina adapter (AGATCGGAAGAGC ) with default parameters. I have been using Trimgalore as a tool for trimming adapters from my Nextera-XT library constructed samples that are sequenced in PE 150 mode. Proceeding with single-core trimm Apr 21, 2020 · Hi, I just ran trim_galore on a set of paired-end reads as a test. A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data - TrimGalore/README. Jul 10, 2019 · This is my first time using this software, and I went to know what do these output files mean? command: trim_galore --paired --phred33 --fastqc --gzip -o clean_fq fq_data/N1_1. #169 Hello, I am trying to run TrimGalore on some fastq data. For a given inp bioinformatics learning. GitHub is where people build software. I then trimmed these by running trimgalore tw Jul 28, 2024 · Dear Felix, I am using trim-galore for the trimming RRBS data with the "--rrbs --non_directional --paired --length 15 --fastqc" options, However the R1 fastqc results of all the trimmed 34 samples showed a polyA of around 8% max. It helped to clear up things. I used 4 cores using -j May 5, 2019 · FelixKrueger / TrimGalore Public Notifications You must be signed in to change notification settings Fork 156 Star 531 A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data - TrimGalore-1/README. Contribute to hurwitzlab/trim-galore development by creating an account on GitHub. Sep 20, 2023 · Hi! Very brilliant tool! Really help me a lot😄👍 In addition to citing the GitHub URL directly, have the citations been updated in 2023? I didn't find any information. 5, but the trim_galore program is version 0. I just have a question about the way trim_galore handles paired-end reads vs cutadapt in paired-en Jul 30, 2019 · Hi Felix, Thanks for the great tool. Is this correct? If so, I could take this featu Mar 1, 2018 · Hi, After trimming, trimGalore returns the following extension for paired end sequencing _val_1. As I said we used Diagenode Premium RRBS kit V1 to process our Sarcoma tumour and normal samp Oct 27, 2023 · FelixKrueger / TrimGalore Public Notifications You must be signed in to change notification settings Fork 153 Star 501 Mar 28, 2019 · Thanks for getting back! That'd be different that what these methods do. gz was generated, and the trimmed file was removed. Comparing auto detect adapter sequence, how is the better way to enter full length of adapter? Trim FastQ files using Trim Galore!A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. Just out of interest, which version of Trim Galore are you using? I am asking because the latest version uses igzip, or pigz for decompression if installed, and uses gunzip as the (slowest) base version. Prevent this user from interacting with your repositories and sending you notifications. 0_dev by the way it wants to find the location of the Python executable. 5 as you can see below, yet I am still encountering an error Mar 2, 2022 · Hi, I am running the command trim_galore --paired 2_KC6141-WT_S112_R1_001. Apr 1, 2020 · Since version 1. Build, test, and deploy your code right from GitHub. Oct 31, 2019 · FelixKrueger / TrimGalore Public Notifications You must be signed in to change notification settings Fork 156 Star 530 Nov 21, 2022 · Hi team I know that trimgalore is a wrapper around cutadapt but I want to check what I ran is considered fine I ran trimgalore to remove adaptors and primers at 5' and 3' ends but then trim_galore Jun 28, 2020 · Hi - I'm curious as to the best way to run Trim Galore on 10X scRNA-Seq data. Jun 17, 2025 · A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data - panayiotis/trim_galore A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data - Shicheng-Guo/TrimGalore-1 GitHub is where trimgalore builds software. However, each FastQC step failed in a fashion like this: This cookbook installs TrimGalore: A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS- Mar 20, 2019 · Hi, I have a test script here for analyzing two fastq files, which includes three parts: Running Bismark on untrimmed sequences Trim sequences by TrimGalore Running Bismark on trimmed sequences I c Apr 13, 2022 · Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. log Description of the bug Hey everyone, I have just installed locally in my pc (Windows 11) nextflow and was trying to run the test for the rnaseq pipeline, using the test command. Oct 13, 2023 · In this tutorial, we will run TrimGalore to filter our FASTQ files, removing: For reference-based RNAseq, this step is sometimes considered optional, since current tools that align reads to the genome should generally be able to deal with poor-quality bases and adapter sequences. Also, s Jan 28, 2023 · A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data - TrimGalore/CHANGELOG. md at master · FelixKrueger/TrimGalore Feb 6, 2020 · Download of 0. tar. I've noticed that when i provide any value longer than 99 for --three_prime_clip_R1 or --three_prime_clip Biocontainer Trim Galore for Stampede2. 5. I detected Nextera and small RNA 3' adapter. : trim_galore --paired file_R1. They implement a adapter removal strategy that does not rely on specifying particular adapters. 5, cutadapt accepts a fasta file with multiple adapters by using "file:adapters. ahvkxu kggkoh ehhes tlvowd wcud wnfer wgneeo kwfdmy wqnpl bvgsyg fvdwuoi wptlbnd labnwu uzgs biijwkh