<div dir="ltr">Hi,<div><br><div>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.</div><div><br></div><div><pre style="font-family:Consolas,'Andale Mono WT','Andale Mono','Lucida Console','Lucida Sans Typewriter','DejaVu Sans Mono','Bitstream Vera Sans Mono','Liberation Mono','Nimbus Mono L',Monaco,'Courier New',Courier,monospace;font-size:12px;margin-top:0px;margin-bottom:0px;padding:12px;line-height:1.5;overflow:auto;color:rgb(64,64,64)">miso --run mm9/pickled/SE data/control.bam --output-dir SE/control/ --read-len 35 --paired-end 250 15</pre></div><div>I generated the GFF index files:</div><div>
<p>index_gff --index miso/miso_install/lib/python2.7/site-packages/misopy/gff-events/mm9/SE.mm9.gff
indexed/ </p><p>and the index directory was created in the current working directory:</p><p>ls -l indexed/</p><p>total 6684</p><p>drwxr-xr-x 2 agarw005 agarw005 73728 May 26 17:02 chr1</p><p>drwxr-xr-x 2 agarw005 agarw005 69632 May 26 17:02 chr10</p><p>...</p><p>-rw-r--r-- 1 agarw005 agarw005 12288 May 26 17:02 compressed_ids_to_genes.shelve</p><p>-rw-r--r-- 1 agarw005 agarw005 1904397 May 26 17:02 genes.gff</p><p>-rw-r--r-- 1 agarw005 agarw005 5185536 May 26 17:02 genes_to_filenames.shelve</p><div>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.</div><div><br></div><div>Thanks,</div><div><br></div><div>- Pankaj</div><p><font size="1">--------------------------------------</font></p><p><font size="1" face="georgia, serif">Pankaj Agarwal, M.S</font></p><p><font size="1" face="georgia, serif">Bioinformatician</font></p><p><font size="1" face="georgia, serif">Database Analyst II</font></p><p><font size="1" face="georgia, serif">Surgical Sciences – Applied Therapeutics</font></p><p><font size="1" face="georgia, serif">Department of Surgery</font></p><p><font size="1" face="georgia, serif">Duke University</font></p><p><font size="1" face="georgia, serif">919-244-6389</font></p><p><font size="1" face="georgia, serif"><a href="mailto:p.agarwal@duke.edu">p.agarwal@duke.edu</a></font></p></div><div><font face="georgia, serif"><br></font></div><div><br></div></div></div>