[miso-users] errors with run_events_analysis

[Yarden Katz]

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
>> 
>> 
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