[miso-users] Miso Example

[Yarden Katz]

Hi Pankaj,

The file name is just an example filename, it is not provided in the examples.  In the future we will include example BAM files, but that was meant to just be an illustration of comparing two BAM files that are provided by the user.  Any BAM file that matches the GFF annotation chromosome naming will do.

Best, Yarden

On May 26, 2015, at 5:18 PM, Pankaj Agarwal <bioinformatics.cancer at gmail.com> wrote:

> Hi,
> 
> I am just getting started with MISO to use it for alternate splicing analysis.  Installation of MISO was easy.  I am now trying to run the example given in the documentation.
> 
> miso --run mm9/pickled/SE data/control.bam --output-dir SE/control/ --read-len 35 --paired-end 250 15
> I generated the GFF index files:
> index_gff --index miso/miso_install/lib/python2.7/site-packages/misopy/gff-events/mm9/SE.mm9.gff indexed/ 
> 
> and the index directory was created in the current working directory:
> 
> ls -l indexed/
> 
> total 6684
> 
> drwxr-xr-x 2 agarw005 agarw005   73728 May 26 17:02 chr1
> 
> drwxr-xr-x 2 agarw005 agarw005   69632 May 26 17:02 chr10
> 
> ...
> 
> -rw-r--r-- 1 agarw005 agarw005   12288 May 26 17:02 compressed_ids_to_genes.shelve
> 
> -rw-r--r-- 1 agarw005 agarw005 1904397 May 26 17:02 genes.gff
> 
> -rw-r--r-- 1 agarw005 agarw005 5185536 May 26 17:02 genes_to_filenames.shelve
> 
> But I cannot find the BAM file "control.bam" anywhere in the installation.  I could not find any other mention of this example BAM files in the docs about where to download.  Can someone please let me know how I could get this file so I could run the test and get started using MISO.
> 
> Thanks,
> 
> - Pankaj
> --------------------------------------
> 
> Pankaj Agarwal, M.S
> 
> Bioinformatician
> 
> Database Analyst II
> 
> Surgical Sciences – Applied Therapeutics
> 
> Department of Surgery
> 
> Duke University
> 
> 919-244-6389
> 
> p.agarwal at duke.edu
> 
> 
> 
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