I hope there is someone out there that can help me. I have been struggling to use gmapper (SHRIMP2) to do some alignment on SOLiD colorspace files.
This is the top few lines of my fastq file (First question - is this actually colorspace?):
This is my command line:
gmapper-cs --no-qv-check -Q -N 8 -o 5 -h 80% SRR553457.fastq /users/njss3/PTESFinder/data/chr1_GL383518v1_alt.fa >SRR553457.sam 2>SRR553457.log
note: detected fastq format in input file [SRR553457.fastq]
- Processing read file [SRR553457.fastq]
done r/hr r/core-hr
There has been a problem reading in the read "SRR553457.1", the quality length exceeds the sequence length!
Are you using the right executable? gmapper-cs for color space? and gmapper-ls for letter space?
This is the error I am getting in the log file: