Hi, I used blasr aligner to align a pacbio dataset against a reference. I used *.bax.h5 files for the alignemnt. Since there were three *.bax.h5 file for a single sample I used the command as follows:
blasr m160128_145513_42215_c100901562550000001823208404291605_s1_p0.1.bax.h5 m160128_145513_42215_c100901562550000001823208404291605_s1_p0.1.bax.h5 m160128_145513_42215_c100901562550000001823208404291605_s1_p0.1.bax.h5 query.fasta -sam -unaligned unaligned.reads -nproc 8 -out output.sam
I converted the sam to bam and sorted it. Now, when I check the bam file for the counts of read mapped/unmapped, I get something like this:
samtools view -c -F 4 output.sorted.bam 12978
but when I use a different approach of counting reads I get 3 different values:
samtools view -F 4 output.sorted.bam | wc 12978 298494 9212184
I am not able to understand if these 3 values belong to individual *.bax.h5 I originally used in the mapping or this something else?
is there any other way to use 3 bax.h5 file together in the same mapping step?