Yeah, you'll need to sort and index the file. You'd also need that to view
the file in IGV or any other similar browser, since they all require quick
random access, which is afforded by sorting and indexing.
Devon
--
Devon Ryan, Ph.D.
Email: [email protected]
Laboratory for Molecular and Cellular Cognition
German Centre for Neurodegenerative Diseases (DZNE)
Ludwig-Erhard-Allee 2
53175 Bonn
Germany
<[email protected]>
On Wed, Aug 6, 2014 at 12:14 PM, Aakriti Jain <[email protected]>
wrote:
> 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 <[email protected]> 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: [email protected]
> Laboratory for Molecular and Cellular Cognition
> German Centre for Neurodegenerative Diseases (DZNE)
> Ludwig-Erhard-Allee 2
> 53175 Bonn
> Germany
> <[email protected]>
>
>
> On Wed, Aug 6, 2014 at 11:34 AM, Aakriti Jain <[email protected]>
> 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
>>
>> ------------------------------------------------------------------------------
>> Infragistics Professional
>> Build stunning WinForms apps today!
>> Reboot your WinForms applications with our WinForms controls.
>> Build a bridge from your legacy apps to the future.
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk
>> _______________________________________________
>> Samtools-help mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/samtools-help
>>
>
>
>
------------------------------------------------------------------------------
Infragistics Professional
Build stunning WinForms apps today!
Reboot your WinForms applications with our WinForms controls.
Build a bridge from your legacy apps to the future.
http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk
_______________________________________________
Samtools-help mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/samtools-help
