<html><head><style type='text/css'>p { margin: 0; }</style></head><body><div style='font-family: arial,helvetica,sans-serif; font-size: 12pt; color: #000000'>Dear MISO users,<br><br>I recently started using MISO with input data from strand-specific libraries. I configured MISO accordingly by setting "strand = fr-secondstrand".<br><br>When inspecting the batch-logs generated by run_events_analysis.py, I noticed the following curious behaviour:<br>* For the vast majority of events on the - strand, nearly all reads are discarded due to strand violation (example below)<br>* For events on the + strand, only few reads are discarded by this filter.<br><br>I visually inspected the reads of the BAM file together with the annotation in IGV and both looked correct regarding strandedness.<br><br>Can someone please explain me this behaviour? I am using version 2 of mm10 alternative events and MISO version 0.4.9.<br><br>Thanks a lot in advance.<br><br>Best,<br>Andreas<br><br><br>Example output of run_events_analysis.py:<br>
Computing Psi for 1 genes...<br>
- 1:97661831:97662018:-@1:97654600:97654689:-@1:97643902:97646361:-<br>
...<br>
Filtered out 61 read pairs that were on same strand.<br>
Filtered out 60 reads that had no paired mate.<br>
- Total read pairs: 2458<br>
No. reads discarded due to strand violation: 2458<br>
Only 0 reads in gene, skipping (needed >= 20 reads)<br></div></body></html>