Re: [Samtools-help] samtools tview : fail to load bam index

[Tom B. <tb...@um...>]

I think this is the expected tview display.  Please see 
the section for samtools pileup in the samtools man page.

 	 	 	 	 	-  tom blackwell  -

On Mon, 12 Apr 2010, Dieter Best wrote:

> Hi there,
>
> thanks for all the help. - I hadn't sorted and indexed the bam file.
>
> Now I can see something with samtools tiew.
>
> However, for the reads I see only dots (.) and commas (,),
> occasionally a letter.
>
> Any ideas what that might be due to?
>
> Thanks again for responding.
>
> -- Dieter
>
>
> On Fri, Apr 9, 2010 at 12:50 PM, Tom Blackwell <tb...@um...> wrote:
>> Dieter  -
>>
>> I think that 'samtools tview' requires the .bam file to be already sorted by
>> genome position ('samtools sort') and also requires a .bai index file
>> ('samtools index') for quick access to selected regions.  If there is not a
>> .bai file already, 'samtools tview' will silently call 'samtools index' to
>> create one.  But in order for this to work, samtools needs to have write
>> permission in the directory where the sorted .bam file is.  Any of these
>> steps might be going wrong for you.
>>
>>                                        -  tom blackwell  -
>>
>> On Fri, 9 Apr 2010, Dieter Best wrote:
>>
>>> Hello there,
>>>
>>> I am having some trouble with samtools tview.
>>> Here is the chain of events (I align some reads with bowtie 0.11.3)
>>>
>>> $ bowtie --sam $GENOME $READS nminus_bowtie.sam
>>> $ samtools view -bS -o nminus_bowtie.bam nminus_bowtie.sam
>>> [samopen] SAM header is present: 765 sequences.
>>> $ samtools tview nminus_bowtie.bam
>>> [bam_index_load] fail to load BAM index.
>>> $ which samtools
>>> /data/software/samtools-0.1.7a/samtools
>>>
>>> What am I doing wrong?
>>>
>>> Thanks in advance.
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Download Intel&#174; Parallel Studio Eval
>>> Try the new software tools for yourself. Speed compiling, find bugs
>>> proactively, and fine-tune applications for parallel performance.
>>> See why Intel Parallel Studio got high marks during beta.
>>> http://p.sf.net/sfu/intel-sw-dev
>>> _______________________________________________
>>> Samtools-help mailing list
>>> Sam...@li...
>>> https://lists.sourceforge.net/lists/listinfo/samtools-help
>>>
>>>
>>>
>>
>
>
>
> -- 
> http://www.linkedin.com/in/dieterbest
>
>
>