make.fastq for each sample

Commands in mothur
1

I would like to get a fastq file for each of my biological samples.

I can get the fastq for the whole dataset file using make.fastq, but then split.group does not work because it only reads a fasta file as input. Alternatively, I first used split.groups and deunique.seqs to get the fasta file for each sample but I was not able to use those commands with the qual file for the whole dataset to get the corresponding qual files for each sample.

What do you recommend to do?
Thanks

2

At this point you’d probably have to write your own scripts to do this.

3

I am trying to submit 454 data to the SRA. They want either bam, fastq, or sff.
My sff file contains data for many samples, including samples which I did not plan to submit to the SRA. Is there a way to split the sff file using the barcode?
Another mothur user already asked this question a while ago:
http://mothur.ltcmp.net/t/split-sff-files/954/2
are the trim.flow files we obtain after running trim.flows related to sff files?
Thanks a lot

4

Try running sffinfo with your oligos file adn the typical “diffs” options and this will generate the appropriate sff files.

5

We want to pull out select samples to submit to SRA, too, but we do not have the .sff files. We only have .fna and .qual files. Is it possible to make .fastq of just a portion of samples with these files as input? Thanks for your help!

6

http://www.mothur.org/wiki/Make.fastq

7

thanks for the tip! running sffinfo with sfftxt=T worked.

8

Maybe late for amymarie

but useful for future analysis. Use the following command:

trim.seqs(fasta=“name of file”.fas, oligos=“name of file”.oligos, qfile=“name of file”.qual, allfiles=t)


This will generate a .fas and qual file for each sample. Then used the make.fastaq command (http://www.mothur.org/wiki/Make.fastq) for each set of .fas and .qual files representing a particular sample. This will generate a fastq file for each sample.
This is useful for SRA submission with 454 technology.