Question

fqtrim minimum read length default value

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9.7 years ago

hana ▴ 190

Hi everyone

I would like to use fqtrim to trim my RNA seq raw data. The default minimum read length after trimming is 16. Can anyone explain this default value for me.

Thanks in advance you

RNA-Seq • 2.3k views

ADD COMMENT • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by hana ▴ 190

Ram · Answer 1 · 2015-03-04

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9.7 years ago

GouthamAtla 12k

This means any reads that gets shortened less than 16bp will be removed. Its clearly stated in manual.

minimum read length after trimming; if the read sequence is shorter than this, before or after the requested trimming filters, the read is discarded (trashed). Default: 16.

In other words, the shorted read will be 16bp after the trimming. All reads less than 16bp will be discarded.

ADD COMMENT • link 9.7 years ago by GouthamAtla 12k

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Thank you for your comment. I mean why the default is 16 rather that 24 or another number?

ADD REPLY • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by hana ▴ 190

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Default values will works for most of the datasets. They must have found it optimal value while testing the tool on a particular data set. BUT IT HIGHLY VARIABLE BETWEEN DATASETS. If they do not keep default values, you may need to enter tons of values while running the command.

ADD REPLY • link 9.7 years ago by GouthamAtla 12k