trim.seqs: names file??

Commands in mothur
1

Hi

I have no flow data and therefore want to do filtering using the qual files and fasta files. I followed the 454 SOP at this step, but I got the group file and now I wander how to get the names file? with shhh.flows you get the names file as output, but directly with trim.seqs only the group file. How should I do to continue the SOP without a names file?

Thank you!

Susana

2

Hi Susana
unique.seqs will generate the name file for you.

Ido

3

Thank you Ido for your answer. But… then, how am I suppossed to run unique.seqs? If I follow the 454 SOP, I should run it with the fasta and names files :frowning:

mothur > unique.seqs(fasta=GQY1XT001.shhh.trim.fasta, name=GQY1XT001.shhh.trim.names)

Susana

4

If you start here:

http://www.mothur.org/wiki/454_SOP#Using_quality_scores

You’ll see that you don’t need to use a names file to run trim.seqs. You will need to adjust the names accordingly for the rest of the SOP.

Pat

5

Hi Pat

Not to run trim.seqs, that I have already done with fasta, oligos and qual files. The question is how to continue from here as trim.seqs only gave a group file but not a names file, to use in the next unique.seqs command, as in the SOP. If you use the qual files and not the secon option in the SOP to use when the qual files are not available, trim.seqs outputs only a group but not a names file, unless I did sth wrong?

Sus

6

Hi Susana
When you run unique.seqs for the first time your fasta file contains all reads, the command will generate a name file for you which will account for the names of all the seq each unique seq represents and generate a new fasta file with only unique seqs.
In other words chillax all will be well, just run it w/o the name file.

Ido

7

Thank you Ido for explaining that to me!

I thought the names file was needed, as it was indicated in the SOP that I should include it. I will follow then as you suggested.

Bye,

Susana