[miso-users] errors with run_events_analysis

[Yarden Katz]

Hi Maayan,

I think it's a bug with chromosome naming of the index files that was introduced a while ago and was fixed.  The newest version of MISO (in github) should have better error handling.  But to be sure, could you please tell me how your indexed chromosome directories are named, i.e. what is:

$ ls /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/ 

Finally, the easiest way to get to the bottom of it is if you send me the GFF you used (I assume it's from an Ensembl annotaton) and any small portion of the BAM.  I don't need the whole BAM, you can simply take out any segment of it that has the headers, e.g. one chromosome's worth of reads or even less, such as:

# pulls out all of chromosome 1
$ samtools view -bh yourbam.bam 1 -o test.bam

# pulls out a segment of chromosome 1, bases 1-10000000
$ samtools view -bh yourbam.bam 1:1-10000000 -o test.bam

A small BAM segment reveals nothing of anything and I assure you I will delete it once I get to the bottom of this bug.  I'm sure that this will be trivial to fix (if it isn't already fixed in the latest GitHub version).

   --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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