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YangLab / CIRCexplorer

A combined strategy to identify circular RNAs (circRNAs and ciRNAs) (Zhang et al., Complementary Sequence-Mediated Exon Circularization, Cell (2014), 159:134-147)
http://yanglab.github.io/CIRCexplorer
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Bam file error #10

Closed averm22 closed 8 years ago

averm22 commented 8 years ago

I have run the tophat commands and generated bams using tohat2 fusion search on the unmapped fastq. However, running them with the CIRCexplorer now gives the error - "Please make sure sample is BAM!"

Does the bam file obtained from tophat2 fusion need to be processed in any other way before passing it to the CIRCexplorer

Thanks

kepbod commented 8 years ago

From your error information, your CIRCexplorer parameters contain -f sample or --fusion=sample, so please check the sample file to make sure that it is the correct TopHat-Fusion bam file.

averm22 commented 8 years ago

Hi

Thanks for the reply. I looked at the code and figured I was using an older version of pysam rather than the one with the function used to check the bam file. It ran very well

Thank you Akanksha

On Oct 9, 2015, at 9:16 PM, Xiao-Ou Zhang notifications@github.com wrote:

From your error information, your CIRCexplorer parameters contain -f sample or --fusion=sample, so please check the sample file to make sure that it is the correct TopHat-Fusion bam file.

— Reply to this email directly or view it on GitHub.