Miso - no events meet read coverage filter

Question

[willtun1991]

Hey

I ran miso with the settings: --run indexed_Ch37_ensembl T0_1.bam --output-dir STAR_T0_output/ --read-len 50 --paired-end 75.4 9.9 --prefilter

...and it produced this error message: - miso_main - ERROR - None of the events in /Users/wt0062/myenv/indexed_Ch37_ensembl appear to meet the read coverage filter. Check that your BAM headers in /Users/wt0062/myenv/T0_1.bam match the GFF headers of indexed events.

How do I check my Bam headers? I cannot seem to open my Bam file in a normal way. How do I subsequently change the headers of my Bam file?

Thanks Will

[francesco.ferrari.1988]

Hi, I am having a similar issue, but I am sure the GFF file used matches with the BAM header. Did you find a way to solve the problem? Thank you so much in advance

Answer 1

[Ram]

Hey,

you can check your bam file header by following command in order you already have samtools.

samtools view bamfile | head