[miso-users] errors with run_events_analysis

[Maayan Kreitzman]

Sorry, I forgot the attachment, here it is.

Unfortunately, I'm not allowed to share the BAM file, since it's private data. 
If you tell me what to look for I'll do my best. 

________________________________________
From: Yarden Katz [yardenny at gmail.com] On Behalf Of Yarden Katz [yarden at mit.edu]
Sent: Thursday, March 21, 2013 1:55 PM
To: Maayan Kreitzman
Cc: Yarden Katz; miso-users at mit.edu
Subject: Re: [miso-users] errors with run_events_analysis

Hi Maayan,

I don't see any attachments in your email?

Also, you can send me the BAM file (e.g. by sharing a link to it via DropBox) and I can take a look.

  --Yarden



On Mar 21, 2013, at 1:10 PM, Maayan Kreitzman wrote:

> Hi Yarden,
>
> As far as I can tell, there are no prefixes in the bam file.
>
> I attached the results from the three commands so you can take a look.
>
> thanks for you help!
>
> Maayan
> ________________________________________
> From: Yarden Katz [yardenny at gmail.com] On Behalf Of Yarden Katz [yarden at mit.edu]
> Sent: Wednesday, March 20, 2013 5:50 PM
> To: Maayan Kreitzman
> Cc: miso-users at mit.edu
> Subject: Re: [miso-users] errors with run_events_analysis
>
> It would also be useful to see:
>
> $ head /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/genes.gff
>
>
>  --Yarden
>
>
>
> On Mar 20, 2013, at 8:46 PM, Yarden Katz wrote:
>
>> Hi Maayan,
>>
>> Can you confirm that your BAM file does not have chr prefixes?  I.e. can you please let me know what the output of these commands are:
>>
>> $ samtools view /projects/mkreitzman_prj/expression_quantification_testing/testing/test_data/strand_specific/JAGuaR_rev_87647/A08586_gr3.neg.bam | head
>>
>> and
>>
>> $ samtools view -H /projects/mkreitzman_prj/expression_quantification_testing/testing/test_data/strand_specific/JAGuaR_rev_87647/A08586_gr3.neg.bam
>>
>> Best, --Yarden
>>
>>
>>
>>
>> On Mar 20, 2013, at 8:35 PM, Maayan Kreitzman wrote:
>>
>>> Hi everyone,
>>>
>>> I'm new to MISO, and would like some help. I've successfully installed misopy-0.4.7.
>>>
>>> I also downloaded and indexed the ensembl gff3 (no "chr" in the chromosome names).
>>> The next step isn't working though. My library is a paired-end strand specific library.
>>>
>>> The command I ran is this:
>>>
>>> python misopy/run_events_analysis.py --paired-end 75 8 --compute-genes-psi /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/ /projects/mkreitzman_prj/expression_quantification_testing/testing/test_data/strand_specific/JAGuaR_rev_87647/A08586_gr3.neg.bam --output-dir /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/results --read-len 100 &> /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/results/A08586.log
>>>
>>> the errors I get look like this (I've attached the full std out + stderr):
>>> Traceback (most recent call last):
>>> File "/projects/mkreitzman_prj/expression_quantification_testing/misopy-0.4.7/misopy/run_miso.py", line 488, in <module>
>>>  main()
>>> File "/projects/mkreitzman_prj/expression_quantification_testing/misopy-0.4.7/misopy/run_miso.py", line 432, in main
>>>  run_compute_genes_from_file(options)
>>> File "/projects/mkreitzman_prj/expression_quantification_testing/misopy-0.4.7/misopy/run_miso.py", line 247, in run_compute_genes_from_file
>>>  event_type=options.event_type)
>>> File "/projects/mkreitzman_prj/expression_quantification_testing/misopy-0.4.7/misopy/run_miso.py", line 128, in compute_gene_psi
>>>  gene_obj)
>>> File "/home/mkreitzman/.local/lib/python2.7/site-packages/misopy-0.4.7-py2.7-linux-x86_64.egg/misopy/sam_utils.py", line 191, in fetch_bam_reads_in_gene
>>>  chrom = chrom_parts[1]
>>> IndexError: list index out of range
>>>
>>> The bam file is position sorted and has a .bai in the same folder. The parameters for the --paired-end are just off the top of my head, but I tried without this option at all and the same thing happens.
>>>
>>> Thanks in advance for any ideas you may have.
>>>
>>> Maayan<A08586.log>_______________________________________________
>>> miso-users mailing list
>>> miso-users at mit.edu
>>> http://mailman.mit.edu/mailman/listinfo/miso-users
>>
>>
>> _______________________________________________
>> miso-users mailing list
>> miso-users at mit.edu
>> http://mailman.mit.edu/mailman/listinfo/miso-users
>

-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: for_yarden.txt
Url: http://mailman.mit.edu/pipermail/miso-users/attachments/20130321/0fc9e3e5/attachment-0001.txt