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DaehwanKimLab / hisat-genotype

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Gene expression using BAM files from HISAT-genotype #43

Open Tijs-dot opened 3 years ago

Tijs-dot commented 3 years ago

Hi Chris,

I have used HISAT-genotype successfully to call the HLA types for my dataset. Now I want to use the BAM files for gene expression analysis, but the format does not seem to work for featureCounts, the output are all zeroes. Do you know what could cause this? Can the hla-extracted BAM files be used for expression analysis?

Thanks, Tijs

chbe-helix commented 3 years ago

Hi Tijs,

Sorry for the late reply. The BAM files are directly from HISAT2 alignment to a genotype genome. This genome has some positional offset to the GRCh38 reference. I suspect the outputs are zero because the alignment positions are off of the feature inputs you want counted.

Thanks, Chris