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<body class='hmmessage'><div dir='ltr'><div>Hi all, I'm running MISO but constantly getting no events found, that means in <span style="font-size: 12pt;">miso_output/ I have a list of subfolders:</span></div><div><span style="font-size: 12pt;">batch-genes batch-logs cluster_scripts scripts_output</span></div><div><span style="font-size: 12pt;">with a list of </span><span style="font-size: 12pt;">batch-X_genes.txt files in </span><span style="font-size: 12pt;">batch-genes.</span></div><div><span style="font-size: 12pt;"><br></span></div><div><span style="font-size: 12pt;">But in miso_comopare the file </span><span style="font-size: 12pt;">.miso_bf have no values besides the column head. Could sb advise me about possible causes? Thank you.</span></div><div><span style="font-size: 12pt;"><br></span></div><div><span style="font-size: 12pt;">Regards,</span></div><div><span style="font-size: 12pt;">Long</span></div><div><br></div><div><br></div><div><br></div><div>Following is part of the output of my sh:</div><div><br></div><div>The end which indicates no event found: </div><div><br></div><div>Retrieving MISO files in sample directories...</div><div>Computing sample comparison between /ifshk1/ST/COMG/PMO/long/splicingSamples/miso_output/SE/CH20N and /ifshk1/ST/COMG/PMO/long/splicingSamples/miso_output/SE/CH20T...</div><div> - No. of events in /ifshk1/ST/COMG/PMO/long/splicingSamples/miso_output/SE/CH20N: 0</div><div> - No. of events in /ifshk1/ST/COMG/PMO/long/splicingSamples/miso_output/SE/CH20T: 0</div><div>Creating comparisons parent directory: /ifshk1/ST/COMG/PMO/long/splicingSamples/miso_compare/SE/CH20/CH20N_vs_CH20T</div><div>Compared a total of 0 events.</div><div><br></div><div><br></div><div>The beginning :</div><div><div>Computing Psi values...</div><div> - GFF index: /ifshk1/ST/COMG/PMO/long/annotationFile/hg19/indexedSEhg19</div><div> - BAM: /ifshk1/ST/COMG/PMO/long/splicingSamples/RNA/CH20N.rna.bam</div><div> - Read length: 90</div><div> - Output directory: /ifshk1/ST/COMG/PMO/long/splicingSamples/miso_output/SE/CH20N</div><div>Checking your GFF annotation and BAM for mismatches...</div><div>Checking if BAM has mixed read lengths...</div><div>Found reads of length 90 in BAM.</div><div>WARNING: No genes.gff file found in /ifshk1/ST/COMG/PMO/long/annotationFile/hg19/indexedSEhg19. Did you index your GFF with an older version of MISO?</div><div>Mapping genes to their indexed GFF representation, using /ifshk1/ST/COMG/PMO/long/annotationFile/hg19/indexedSEhg19</div><div>Searching for /ifshk1/ST/COMG/PMO/long/annotationFile/hg19/indexedSEhg19/genes_to_filenames.shelve..</div><div> - Found shelved file.</div><div>Preparing to run 212 batches of jobs...</div><div>Running batch of 200 genes..</div><div> - Executing: python /ifshk1/ST/COMG/PMO/long/software/python2/lib/python2.7/site-packages/misopy-0.5.2-py2.7-linux-x86_64.egg/misopy/run_miso.py --compute-genes-from-file "/ifshk1/ST/COMG/PMO/long/splicingSamples/miso_output/SE/CH20N/batch-genes/batch-0_genes.txt" /ifshk1/ST/COMG/PMO/long/splicingSamples/RNA/CH20N.rna.bam /ifshk1/ST/COMG/PMO/long/splicingSamples/miso_output/SE/CH20N --read-len 90 --paired-end 250.0 15.0 --settings-filename /ifshk1/ST/COMG/PMO/long/software/python2/lib/python2.7/site-packages/misopy-0.5.2-py2.7-linux-x86_64.egg/misopy/settings/miso_settings.txt</div></div> </div></body>
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