[miso-users] Running MISO with STAR

[CSHL (klin)]

Hi all,

I am running MISO to reproduce published data. I am using STAR aligner and "Human genome (hg19) alternative events v2.0”. The chromosome names were identical (without “chr”), but MISO detected no reads from the sorted bam files generated by STAR. An example message is shown below:

Computing Psi for 1 genes...
 - 10:90424146:90424248:+ at 10:90425236:90425316:+ at 10:90427044:90427159:+
 - GFF filename: /home/miso/hg19/chr10/10:90424146:90424248:+ at 10:90425236:90425316:+ at 10:90427044:90427159:+.pickle
 - BAM: /home/alignment/star/WT.Aligned.sortedByCoord.out.bam
 - Outputting to: /home/alignment/miso/WT
 - Paired-end mode:  (250.0, 15.0)
Loading BAM filename from: /home/alignment/star/WT.Aligned.sortedByCoord.out.bam
Filtered out 0 read pairs that were on same strand.
Filtered out 0 reads that had no paired mate.
 - Total read pairs: 0
No. reads discarded due to strand violation: 0
Only 0 reads in gene, skipping (needed >= 20 reads)

I uploaded an example of the alignment results if you want to test.

https://app.box.com/s/5rtvdp1vivhsn2ef655q4bmidlkx2iqz <https://app.box.com/s/5rtvdp1vivhsn2ef655q4bmidlkx2iqz>

Could you please enlighten me what I did wrong?

Sincerely,
Woody

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