[miso-users] errors with run_events_analysis

[Yarden Katz]

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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