I have read through the bfast manual and although I generally find it very informative, I think it is unclear how SOLiD mate-pairs should be treated in the solid2fastq step. My SOLiD reads files have the following format: F3 and R3 mates are on the same rows of two separate files.
What are the requirements for successful fastq conversion of such files, keeping mate-pair information in the conversion process?
Should the names of mates be identical or is it ok to keep the F3 and R3s?
Should the pairs be placed next to each other prior to conversion in one file, as is exemplified in Figure 4.4 (depicting the resulting fastq file for Illumina reads)?
Regards
//Carl
What are the requirements for successful fastq conversion of such files, keeping mate-pair information in the conversion process?
Should the names of mates be identical or is it ok to keep the F3 and R3s?
Should the pairs be placed next to each other prior to conversion in one file, as is exemplified in Figure 4.4 (depicting the resulting fastq file for Illumina reads)?
Regards
//Carl
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