Entering edit mode
3.0 years ago
CY ▴ 710
This is maybe a silly question. But I just realize that the FASTQ contains both DNA reads of both strand (forward and reverse). However when doing alignment, the strandness of each read is not provided. How does aligner determine the strandness of reads? I am sensing I missed something here.
bwahelp page says this:
bwa paper says " The reverse complemented read sequence is processed at the same time". So
bwawas probably RC'ing the reads when originally released but now may not be doing that. Someone will need to look in the code and confirm.
bowtie/bowtie2store forward and reverse copies in separate index files.
BBMap concatenates the reference chromosomes in a long string. Since it stores its index in a special file format I am not sure if it is storing RC index copy or not.