Hello dear Bio masters,
I'm analyzing some reads from a bacterial genome (E. coli), and I'm trying to get the pileup to calculate coverage for a specific region from a bam file. However, whenever I check the header of my file it has the form:
samtools view -H coli.sorted.bam @SQ SN:gi|49175990|ref|NC_000913.2| LN:4639675 @PG ID:bwa PN:bwa VN:0.5.9-r16
And when I try to retrieve the information from my region (1670-2550) of interest using the "chromosome name" after the SN
samtools view -u coli.sorted.bam gi|49175990|ref|NC_000913.2|:1670-2550 | samtools pileup - > pileup.txt
-bash: 49175990: command not found -bash: ref: command not found -bash: NC_000913.2: command not found -bash: :190-255: command not found [bam_header_read] invalid BAM binary header (this is not a BAM file). [bam_pileup] fail to read the header: non-exisiting file or wrong format. [main_samview] fail to get the reference name. Continue anyway
So it is not accepting the gi|49175990|ref|NC_000913.2| as a name for search. If I omit it I get:
samtools view -u coli.sorted.bam 1670-2550 | samtools pileup - > pileup.txt [main_samview] fail to get the reference name. Continue anyway.
And my file is empty. What am I doing wrong????? Any help will be highly appreciated.