Question: 'Seqtk Trimfq' Truncates Sequence Names In Fastq Files
2
gravatar for knhai45
4.2 years ago by
knhai4520
Kobe, Japan
knhai4520 wrote:

I am processing fastq files from illumina HiSeq1500. I used 'seqtk trimfq' to trim a few first last bases out, but found that the first line of each sequence in fastq files causes a truncation - the part shown in bold/italic get deleted. Does anybody here have a clue of how I can maintain this part even after running seqtk? I will really appreciate your input.

@HWI-1KL121:57:C0M56ACXX:8:1101:1148:2123 1:N:0:AGTCAA CCAGACTTGAGAAGTTCAGCATGGATGCCACAGATCCCTGGAGCTTTGCCCCGTTTCAACTGGNNNNNCGAAGTCCGTGTTTCCCCAAGCGAAGGTGGACC + @@@DDDDDFHBAFHEHAAHG4CBHEDFBFDH)?9CAFDH933?DH?D4?FHBFFGCH@DHIEG#####--(,;=@:;;==?CA:(59(9?@80559ABBCC

illumina fastq • 1.7k views
ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by knhai4520
2
gravatar for Vince Buffalo
4.2 years ago by
Vince Buffalo460
Davis, CA
Vince Buffalo460 wrote:

Hi knhai45,

I just made the correction Heng Li's awesome toolkit. Here's the pull request but in the meantime you could use my version.

ADD COMMENTlink written 4.2 years ago by Vince Buffalo460

nice work, thanks for the improvements!

ADD REPLYlink written 4.2 years ago by Istvan Albert ♦♦ 73k
0
gravatar for knhai45
4.2 years ago by
knhai4520
Kobe, Japan
knhai4520 wrote:

Hi Vince,

Thank you very much for your quick response and the fix. It works perfectly now.

Best wishes,

knhai45

ADD COMMENTlink written 4.2 years ago by knhai4520

Hi knhai45. Please use the "Add a new anwser to the question!" only for real answers. Use the "Comment" button below an existing answer or comment to add your comment instead. This answer will be deleted.

ADD REPLYlink written 4.2 years ago by Eric Normandeau9.5k
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