Finally I got miso running, however when I am running MISO in paired end mode I am getting two errors and almost all reads are getting filtered out. Error 1. Filtered out N read pairs that were on same strand. Error 2. Filtered out X reads that had no paired mate.
Commands I have used
python ~misopy/run_miso.py --compute-genes-from-file "~batch-genes/batch-0_genes.txt" ~accepted_hits.bam ~MISO_Out --read-len 49 --paired-end 147.0 27.0 --settings-filename miso_settings.txt
What can be done in this case.
Thanks in advance