faxtx_clipper algorithm

[lran2008]

See post #7 in this thread: http://seqanswers.com/forums/showthread.php?t=24450

Also: http://seqanswers.com/forums/showthread.php?t=16056

You may want to try trimmomatic or cutadapt in addition as suggested.

Thans. I tried cutadapt. Its' parameters are easier to understand.

[GenoMax]

See post #7 in this thread: http://seqanswers.com/forums/showthread.php?t=24450

Also: http://seqanswers.com/forums/showthread.php?t=16056

You may want to try trimmomatic or cutadapt in addition as suggested.

[lran2008]

Hi,

I am new to miRNA seq analysis. Now I want to use fastx_clipper to trim the adapters from my miRNA seq data. For fastx_clipper, there is an argument:
[-M N] = require minimum adapter alignment length of N.

At beginning, the parameters I used is :
fastx_clipper -v -Q 33 -l 18 -v -a TGGAATTCTCGGGTGCCAAGG -c

But when I add the argument -M 8, the results would not be the same. Actually another 2000 reads were clipped.

Can anyone tell me the default -M N value in this tool? And how does it work?

Thanks.