Hi Aakriti,
The -t option takes a file argument, which is probably causing your
problem. You likely just want:
samtools view -Sb agaA_1_local.sam > agaA_1_local.bam
Bowtie2 outputs SAM files with a header, so there's generally no reason to
replace it with the -t option.
Best,
Devon
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Laboratory for Molecular and Cellular Cognition
German Centre for Neurodegenerative Diseases (DZNE)
Ludwig-Erhard-Allee 2
53175 Bonn
Germany
<devon.r...@dzne.de>
On Wed, Aug 6, 2014 at 11:34 AM, Aakriti Jain <aakriti.jai...@gmail.com>
wrote:
> Hello,
>
> I was wondering if I could get some advice on using samtools properly.
>
> I'm trying to analyze an output file from a Bowtie2 alignment which is in
> .sam format. I first converted the .sam file to .bam using the following
> command:
>
> $ samtools view -S -t -b agaA_1_local.sam > agaA_1_local.bam
>
> and I got the following return line:
> [samopen] SAM header is present: 1 sequences.
>
> I noticed a .bam file in my directory, so I tried to use the following
> line:
>
> $ samtools tview agaA_1_local.bam agaA.fasta
>
> and got the following errors:
> [bam_header_read] EOF marker is absent. The input is probably truncated.
> [bam_header_read] invalid BAM binary header (this is not a BAM file).
>
> I'm not sure what I'm doing wrong? Am I missing some steps? Why is my .bam
> file not an actual BAM file?
>
> Any help on this will be greatly appreciated!
>
> Thank you,
> Aakriti Jain
>
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