mothur

Help please with a command o mothur


Dear college
We have problem with this command Trim.seqs (fasta=M01.fasta, qfile=M01.qual, qaverage=40, oligos= BARCODE.oligos)
Error : In sequence xxxxxxxx xxx xxxx quality score s, expected a number and got >xxx xxxxx xxxx, setting score =0

This type of error typically happens because the files were processed before you start using them in mothur. Is that possible? Can you ask your sequence provider for the raw, unprocessed, data?

It was made by illumina seqs and I don’t have R1 or R2 data, I extracted from the mapping the fasta and fastq and fasta qual.
Thanks

I’d strongly encourage you to try to track down the raw data. I’m not sure how publishable the data will be if you can’t post the raw data to SRA.

Pat

Mmm… that is should it work with data fastq?
How would that be possible in mothur?

I’m not sure what you’re asking, but mothur has a fastq.info command to separate the sequence and quality score data and make.contigs uses fastq files as input. The preferred approach is make.contigs with the original fastq files.

Pat

Hi my raw seqs is single end

Then you would use fastq.info with trim.seqs. But you would still need the original fastq file

Pat