Hi
the latest versions of TopHat do not generate the coverage.wig file. I used the file accepted_hits.bam with samsamtools and bedtools to generate a bedgraph.
But when I looked at it in UCSC GB, I see that some of the junctions did not have reads aligned to them.
Any kind of help will be appreciated.
Joseph
the latest versions of TopHat do not generate the coverage.wig file. I used the file accepted_hits.bam with samsamtools and bedtools to generate a bedgraph.
Code:
samtools sort accepted_hits.bam accepted_hits.sorted genomeCoverageBed -bg -ibam accepted_hits.sorted.bam -g my.genome > accepted_hits.bedgraph
Any kind of help will be appreciated.
Joseph
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