Hello! I'm using this approach to parallelize the alignment of a run of SOLiD mate-pair reads. I converted the reads using solid2fastq, then partitioned the fastq files using the unix split command. I then successfully ran the match step on each partition.
I then realised that solid2fastq placed F3 reads at the beginning of the fastq while R3 at the end, so after spliting the fastq, F3 reads will be separately aligned from R3 reads. It is here suggested that I separately generate a sam file from each partition.
Does this mean that my reads won't be paired? Will samtools or picard pair my reads when I merge my sam files?
Thanks!
Originally posted by nilshomer
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