question about infer_experiment.py

[Tiffany L]

When I ran infer_experiment.py, I got the following error messages: 

Reading reference gene model Homo_sapiens.GRCh38.79.bed ... Done

Loading SAM/BAM file ...  Finished

Total 0 usable reads were sampled

Unknown Data type

The bam/sam file was generated from TopHat2, and sorted by samtools. The original RNAseq data is single-ended. I also tried the bam/sam file generated from STAR and sorted by samtools. But no luck. Could you please let me know what I could've missed? Thank you so much.

Best,

Tiffany

[Tiffany L]

I figured out the problem. I was an easy fix. Thanks!

[Cara Lwin]

May I ask how you fixed it? I am getting the same error.

[bioinformati...@gmail.com]

Hi Cara

Make sure that the chromosome names in BED file and SAM file have the same name they should match if they are like

1 and chr1 , 2 and chr2 ... you will get this error. 

Regards