fqtrim minimum read length default value

Question

[hana]

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

Answer 1

[GouthamAtla]

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.

[hana]

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

[GouthamAtla]

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.