A question about BWA and paired-end reads. In TopHat, one inputs the paired-end fastq file twice and the tool understands you have paired-end reads. I see that in the case of BWA one must align each pair separately. Can somebody give me a hint on how to generate these two matching files from my paired-end one? Thanks. G.
For BWA, you will have to provide all the reads (1 file containing all the forward or _1 reads from the paired ends) belonging to one end of the paired ends in the first step. You will have to redo the same step but this time you need to provide reads from the other end (1 file containing all the reverse or _2 reads from the paired ends). Both of these steps will produce .sai files (1 for each step OR two in total). These two files will be used by BWA sampe and 1 sam file will be produced.
1) bwa aln 1 file containing reads from one end > 1.sai file 2) bwa aln same step for the other end > 2 .sai file 3) bwa sampe 1.sai 2.sai > bam file
Hope this helps you.