Remove "unpaired" reads from quality-filtered pared-end fastq files.
Hi there, I obtained two fastq files from GA paired end run. I filtered each file by quality using fastq tool kit. Then some forward reads may be removed by low quality whereas the reverse counterparts are OK to be remained on the other file, or vice versa. I want to remove those "unpaired" reads from filtered fastq files so that the two new fastq files contain the identical sets of the reads. Is it possible to do it on galaxy? Thank you very much. Hiroki
Not the most convenient solution, but what I normally do in this situation is to combine the two files, filter then split again. There are tools for combining and splitting paired fastq files in Galaxy. Hope it helps, Carlos On Jan 8, 2013 12:55 AM, "柴田 弘紀" <hshibata@gen.kyushu-u.ac.jp> wrote:
Hi there,
I obtained two fastq files from GA paired end run. I filtered each file by quality using fastq tool kit. Then some forward reads may be removed by low quality whereas the reverse counterparts are OK to be remained on the other file, or vice versa.
I want to remove those "unpaired" reads from filtered fastq files so that the two new fastq files contain the identical sets of the reads.
Is it possible to do it on galaxy?
Thank you very much.
Hiroki ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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Hi Hiroki, This question has come up before, and the best advice our team has to offer is that in most cases, filtering the data this way is unnecessary. Still - there are a few methods to do this, but they are tedious to do - one is to basically covert everything to tabular format, extract the IDs, compare and join the datasets with the id lists, then convert back to fastq. Another is the one Carlos brings up - joining, filtering, splitting - but that has not worked for all sequence formats in the past. Neither of these is recommended, but you are of course welcome to test out and try whatever tools/methods you wish to. With most analysis pipelines, is is fine to leave in the extra reads and proceed with the mapping step. Then, after mapping, this would be the next opportunity do some filtering if you wanted to only retain properly paired reads, etc. However, even this is not always necessary - it depends on what analysis you are doing (e.g. not required for RNA-seq analysis). These tool groups manipulate/provide stats on SAM/BAM datasets: NGS: SAM Tools be sure to see -> Filter SAM NGS: Picard (beta) Hopefully this helps! Jen Galaxy team On 1/7/13 9:54 PM, 柴田 弘紀 wrote:
Hi there,
I obtained two fastq files from GA paired end run. I filtered each file by quality using fastq tool kit. Then some forward reads may be removed by low quality whereas the reverse counterparts are OK to be remained on the other file, or vice versa.
I want to remove those "unpaired" reads from filtered fastq files so that the two new fastq files contain the identical sets of the reads.
Is it possible to do it on galaxy?
Thank you very much.
Hiroki ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org
participants (3)
-
Carlos Borroto -
Jennifer Hillman-Jackson -
柴田 弘紀