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Old 03-15-2012, 10:37 AM   #1
CS Student
Location: US

Join Date: Apr 2011
Posts: 20
Default SHRiMP with FASTAQ input

Dear all,

I am trying to run SHRiMP with FASTAQ input files using the -Q option.

Here is the command I am using:

/home/user/SHRiMP_2_2_2/bin/gmapper-ls /home/user/SHRiMP_2_2_2/reads.phi.x.174.fastq /home/user/SHRiMP_2_2_2/phi.x.174.fa -Q -V -N 1 -o 5 -h 80% > /home/user/SHRiMP_2_2_2/output/map.0_to_2499999.out 2> /home/user/SHRiMP_2_2_2/output/map.0_to_2499999.log

And here is the error I am getting:
- Processing genome file [/home/user/SHRiMP_2_2_2/phi.x.174.fa]
- Processing contig phi.x.174
Loaded Genome
note: detected fastq format in input file [/home/user/SHRiMP_2_2_2/reads.phi.x.174.fastq]
- Processing read file [/home/user/SHRiMP_2_2_2/reads.phi.x.174.fastq]
note: quality value format not set explicitly; using PHRED+64done r/hr r/core-hr
The qv-offset might be set incorrectly! Currenty qvs are interpreted as PHRED+64 and a qv of -14 was observed. To disable this error, etiher set the offset correctly or disable this check (see README).

Could you please advise on how to set the qv offset?
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Old 03-15-2012, 11:39 AM   #2
CS Student
Location: US

Join Date: Apr 2011
Posts: 20

I was able to solve this issue using the following two options:

1. --qv-offset 64: Interpret qvs in fastq input as PHRED+<value>. The default is 33 for colour space and 64 for letter space.

2. --ignore-qvs: When input is fastq, completely ignore base/colour qvs from the analysis, as if the input were fasta.
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