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BgeeDB / bgee_pipeline

Source code of the Bgee pipeline used to build the Bgee database
https://www.bgee.org/
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Use human and mouse GTF file with haplotypes #7

Open smoretti opened 6 years ago

smoretti commented 6 years ago

In Ensembl normal GTF files are complemented - for human and mouse - by GTF files with haplotypes (such as HLA/MHC alternative haplotypes). We should use them in order to improve the mapping for those haplotypes and to better defined intergenic regions.

julien-roux commented 6 years ago

This potentially introduces a problem: some reads will be multi-mapping and might be discarded

smoretti commented 6 years ago

Something to test

fbastian commented 6 years ago

Similar discussion here: https://gatkforums.broadinstitute.org/gatk/discussion/11310/about-the-haplotypes-in-hg19-fasta-and-the-gtf-file Botom line, my impression is that either we have to use a tool supporting alt-aware RNA-Seq alignments, or not to add alternative haplotypes.

jwollbrett commented 6 years ago

I didn't know about this multi-mapping problem. Related comment here : http://seqanswers.com/forums/showthread.php?t=72828 Looks like we should not use haplotypes with kallisto.

SFonsecaCosta commented 5 years ago

Maybe MMSEQ tool could be used in this case.