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.
Is this something that MOTHUR can do?
Please let me know
Thanks
Dr Schloss
Thanks for your reply. I used chop.seqs command, but I do not want what chop.seq command is doing.
I used following command
mothur > chop.seqs(fasta=total.fasta, numbases=100, keep=front)
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.
GM0VFN301BWBUZ rank=0254869 x=661.0 y=633.0 length=839
GTAGTCCACGCCGTAAACGATGTCAACTAGCCGTTG
GAATCCTTGAGATCTTAGTGGCGCAGCTAACGCATT
AAGTTGACCGCCTGGGGAGTACGGCCGCAAGGTTAA
AACTCAAATGAATTGACGGGGGCCCGCACAAGCGGT
GGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAAC
CTTACCAGGCCTTGACATCCAAGTGAACTTCCAGAG
ATGGTTAGTGCTCGGTACGACTGAGTACGAAGGTCG
ACGTGCCTAGTCGGACTTGGGTCCGTTCGACGGTCC
TACGGTCGTTCCGGTTGGTACGTAGTGGTTAGGGTT
AAGTTTCCCGGGTTAAACGTCCGGTAACCCCGAACC
CGTTCCGTTAACCCCTTTAGGTTACCCCTTAAGGTA
CCCAACGGTTTACGTACGGGTTTAGGGTCCGTAACG
GTTCCCTAAAAGGGTACGTAAACGTACGGGTCCCGG
TTAGGAACCCGGTAAAACCGGGGACGGAAAAACCGG
GGTTGGGGGAAAGTTGGGGAAACGTTCGAAACGGTT
CCAAAGTTCAACTTCGGGACCCTTTACCGGGCCCCT
TTACGGGGCCCTTAACGGACCGTTAACCGGTACGAC
CGTTAACGAACGTTACGGTAACCGGGTTAACGGTAC
GGGTAACGGGTTAGGACCCGGTTAAAGGGCCCCCGA
AACGGGACCGGGGTTCCGGGAAAAGGGTCCCGTAAA
AGTTCCCCCGTAAAAGGTAAAAACCCCCGGAAAGGT
AAAACCCCGGGTTTAGTTAACCCCGGGTAAGTTACC
CCCGGGGTACTAAACCGGGTTACCCTTA
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.