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?
Question: running MISO with ENSEMBL GTF if reads were aligned against UCSC genome
3.2 years ago by
lavanya.kannan • 10
lavanya.kannan • 10 wrote:
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