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?
Or
is there any other way to use 3 bax.h5 file together in the same mapping step?
Thanks
•
written
by
JstRoRR
man wc
12978 is the number of lines and exactly what samtools view -c ... reported.
298494 is the number of words. This is useless.
9212184 is the number of characters. This is useless.
You probably wanted wc -l rather than just wc.
Ahh silly me. Thanks Devon.
For the second query, can you suggest if using .bax.h5 files this way is the correct way? I have checked the docs but couldn't find anything as how to use multi .bax.h5 files in mapping. The other way I think of is to map individual .bax.h5 files and merge the bam files together.
I unfortunately have no experience with pacbio .bax.h5 files, so I can't give a useful reply. If you create a new question with just that then I expect someone more familiar with pacbio will reply.
Log in to answer this question.
For the second part, you make a file with the list of files to align in it, with the suffix of the file .fofn .
-mark