Hello everyone,
I'm trying to combine the use of bwa and blat but I have a few difficulties to extract the unmapped reads from bwa.
It appears they are in the first .sam file created using bwa bwasw.
I used the command below to filter the SAM file and extract unaligned reads into the file unalntest.bam:
The problem is that when I flagstat it to see how many reads it contains, the soft tells me that there is no read in it.
By the way, I have this message using "samtools view..." (above):
Could someone help me, please? I'm turning mad!
Thanks.
I'm trying to combine the use of bwa and blat but I have a few difficulties to extract the unmapped reads from bwa.
It appears they are in the first .sam file created using bwa bwasw.
I used the command below to filter the SAM file and extract unaligned reads into the file unalntest.bam:
$ samtools view -f 4 /home/biopuce11/Documents/Adam/bwa-0.5.8/aln/aln.sam -t -b -S -o /home/biopuce11/Documents/Adam/bwa-0.5.8/aln/unalntest.bam
By the way, I have this message using "samtools view..." (above):
[bam_header_read] EOF marker is absent.
[bam_flagstat_core] Truncated file? Continue anyway.
[bam_flagstat_core] Truncated file? Continue anyway.
Thanks.
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