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running MISO with ENSEMBL GTF if reads were aligned against UCSC genome

I aligned reads against UCSC genome using STAR, where UCSC gtf was used as reference annotation. As a result, I get the chromosomes in the format "chr1", .... When using pe-utils function in MISO, it is identifying 0 read pairs. I get this error when I tried using both Homo_sapiens.GRCh37.65.gff and hg19_ensGene.gff3 annotation files and also tried the --no-bam-filter option of the pe-utils function. I notice that my bam files also have "chrM". Will removing reads from "chrM" help?

rna-seq miso
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updated by Emily Emily • written by lavanya.kannan • lavanya.kannan

2 answers

Why not just fix the chromosome names?

  1. samtools view -H foo.bam > header
  2. Edit the header (mostly, remove "chr" and convert "chrM" -> "MT")
  3. samtools reheader
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written by Devon Ryan Devon Ryan

You can use the Ensembl File Chameleon to export an Ensembl annotation file with "chr" style names.

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written by Emily Emily

That's an interesting tool. Does it have the name conversions stored somewhere or does it just tack on chr everywhere?

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written by Devon Ryan Devon Ryan

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