Hi Devon,
Thank you for your help. That did help. I had another question — is it
necessary to sort and index the bam file prior to the trying to view it using
the tview command? I tried to use the tview command but it gives me an error:
[bam_index_load] fail to load BAM index.
Thank you,
Aakriti
On Aug 6, 2014, at 12:01 PM, Devon Ryan <dpr...@dpryan.com> wrote:
> 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
>
>
> 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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