'Seqtk Trimfq' Truncates Sequence Names In Fastq Files

Question

[knhai45]

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

Answer 1

[Vince Buffalo]

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.

[Istvan Albert]

nice work, thanks for the improvements!

Answer 2

[knhai45]

Hi Vince,

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

Best wishes,

knhai45

[Eric Normandeau]

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.