Hello everyone,
I have reads from SOLiD sequencing that were in csfasta + .qual files.
After merging them into csfastq format I would like to align them in colorspace to a reference genome. Does the reference genome have to be indexed for this? and how can I do this?
Also, SHRiMP doesn't seem to be too happy about the csfastq format that I'm providing. I'm getting the following error:
"unrecognized character [0] in input file, try disabling auto-detaction."
I'm already disabling auto-detection by using the -Q command to indicate fastq format.
Any help greatly appreciated.
I have reads from SOLiD sequencing that were in csfasta + .qual files.
After merging them into csfastq format I would like to align them in colorspace to a reference genome. Does the reference genome have to be indexed for this? and how can I do this?
Also, SHRiMP doesn't seem to be too happy about the csfastq format that I'm providing. I'm getting the following error:
"unrecognized character [0] in input file, try disabling auto-detaction."
I'm already disabling auto-detection by using the -Q command to indicate fastq format.
Any help greatly appreciated.
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