[miso-users] Miso Example

[Pankaj Agarwal]

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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