I am looking for a command in mothur that can do following task for me
I have a FASTA file (unaligned) that has suppose 1000 seq. All sequences areof varying length say some are 200 bp but some are even 850 bp. I know that anything that is beyond 550 bp is just noise because my primer set does not amplify 550 bp product at all in first place. so I want to kill portion of sequences that are beyond 550 bp because it is just noise. But I want to retain remaining front portion of sequence. So if some seq are more than 550 bp in my data file, I still want to retain them but only up to 550 bp in length.
In my total.txt file there were 7900 seq, when I used above command mothur returned me 7900 seq and all were 100 bp long. That means it trimmed everything down to 100 bp. This is not what I was looking for.
I wanted mothur to kill only sequence portions that exceeds beyond a certain length say 550 bp and retain the remaining portion.
So I want a script that can delete sequence bases if they are exceeding beyond a certain length say 550 bp in my case.
for example
I have such sequences in my data set. I want to keep this seq but not beyond 550 bp. so i want mothur to look for such seq and trim them to 550 bp.
There will be a short option in chop.seqs for the next release which will hopefully be out by the end of next week. Give it a whack and let us know what you think.