Hi all,
Does anyone have experience using BWA to align reads to multiple reference sequences? I am aligning reads from an exon capture run to a transcriptome reference and I'm wondering if a read will only be aligned to a single transcript. Ideally I would want the alignment reported for all transcripts (for multiple splicings) that the read aligns to equally. I'm also curious to how the pileup file would be printed if I carry the bwa sam output from this alignment step through the samtools pipeline... ie will all of the references (each transcript in my case) be placed in a single pileup file, or is there always only one pileup file reported per reference?
Thanks for your help,
Jon
Does anyone have experience using BWA to align reads to multiple reference sequences? I am aligning reads from an exon capture run to a transcriptome reference and I'm wondering if a read will only be aligned to a single transcript. Ideally I would want the alignment reported for all transcripts (for multiple splicings) that the read aligns to equally. I'm also curious to how the pileup file would be printed if I carry the bwa sam output from this alignment step through the samtools pipeline... ie will all of the references (each transcript in my case) be placed in a single pileup file, or is there always only one pileup file reported per reference?
Thanks for your help,
Jon
