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From: Dieter B. <die...@gm...> - 2010-04-09 18:01:30
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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. |
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From: Tom B. <tb...@um...> - 2010-04-09 19:51:06
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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® 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
>
>
>
|
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From: Dieter B. <die...@gm...> - 2010-04-12 18:41:36
|
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® 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
|
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From: Tom B. <tb...@um...> - 2010-04-12 18:55:47
|
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® 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
>
>
> |
|
From: Dieter B. <die...@gm...> - 2010-04-12 19:07:05
|
It is the expected output. Thanks.
On Mon, Apr 12, 2010 at 11:55 AM, Tom Blackwell <tb...@um...> wrote:
>
> 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® 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
>>
>>
>
--
http://www.linkedin.com/in/dieterbest
|
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