Cannot get coverage signal from bam

[Jon]

Hi, 

I'm trying to run geneBody_coverage but keep getting the following error: 

Processing accepted_hits.bam ...

Cannot get coverage signal from accepted_hits.bam ! Skip

Here's the command I used: 

geneBody_coverage.py -r Creinhardtii_281_v5.5.gene.bed -i accepted_hits.bam -o test_output

The bed file is converted directly from the an gff3 file by the gtf2bed < Creinhardtii_281_v5.5.gene.gff3  > Creinhardtii_281_v5.5.gene.bed command and the bam file was generated from TopHat2 mapping.

I'm not sure if it is caused by some formatting problem with my bam file. Besides, before this error occurred, there was actually an error showing "Warning: accepted.bam.bai does not exist! Skip it.", and I somehow fixed it by creating a bai file by using samtools index accepted_hits.bam. Could it be related to the coverage signal problem?

Thank you,

Jon

[Liguo Wang]

Please check if the chromosome IDs are consistent between you BAM file and BED file. 

Liguo

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[Jon]

Hi Liguo,

Thank you for your prompt reply, I tried to look into my BAM file (which I have converted to SAM so I can read it) and the BED file, but I couldn't find any major inconsistency. May I know what "chromosome ID" are you suggesting to check specifically? 

Thank you again,

Jon

 

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