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 [email protected]
_______________________________________________ miso-users mailing list [email protected] http://mailman.mit.edu/mailman/listinfo/miso-users
