Comments (8)
I found that FASTX-toolkit implements this feature.
http://hannonlab.cshl.edu/fastx_toolkit/commandline.html#fastx_trimmer_usage
[-f N] = First base to keep. Default is 1 (=first base).
[-l N] = Last base to keep. Default is entire read.
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This would be useful — I'd be happy to implement this and issue a pull request if it'll be incorporated. Note that bioawk can also do this pretty easily:
$ echo ">test-1\\nAGTATCTAGCATATCGT\\n>test-B\\nGCTAGCACGATC" | \
bioawk -cfastx '{print fastx($name, substr($seq, 0, 10))}' # note this depends on fastx(), a function I implemented
>test-1
AGTATCTAGC
>test-B
GCTAGCACGA
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Release 1.0 does not support trimming to fixed length as adding the functionality may affect the stability of trimfq. You may use Vince's script to achieve the goal for now. I will leave the issue open.
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Actually release 1.0 supports trimming to fixed length!
Just try "seqtk -q 0 -l N input.fq" (it keeps the first N bp)!
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I have just commited some changes which does all these (i.e. shortcircuiting the q == 0, keep first last N bp).
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Implemented via 46cd37e ... after 3 years. Sorry.
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Thanks, Heng!
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Would you please tag a new stable release tagged either 1.1
or 87
? The last stable release 1.0
was tagged in 2013. An out-of-date tagged stable release is more confusing than having no tagged stable release at all.
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