Question: fqtrim minimum read length default value
0
gravatar for hana
5.3 years ago by
hana180
Malaysia
hana180 wrote:

Hi every one

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 • 1.4k views
ADD COMMENTlink modified 5.3 years ago by geek_y11k • written 5.3 years ago by hana180
0
gravatar for geek_y
5.3 years ago by
geek_y11k
Barcelona
geek_y11k wrote:

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 COMMENTlink modified 5.3 years ago • written 5.3 years ago by geek_y11k

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

ADD REPLYlink written 5.3 years ago by hana180

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 REPLYlink written 5.3 years ago by geek_y11k
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