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Old 06-22-2011, 08:30 PM   #1
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Location: China

Join Date: Sep 2009
Posts: 199
Default coveragebed output result problem


I'm running coveragebed to calculate the number of read count in each transcript of tophat alignment result by using the following command:
/bedtool/arq5x-bedtools-26a87ab/bin/coverageBed -abam accepted_hits.bam -b transcripts.bed > transcripts.cov.txt 
cat transcripts.cov.txt
gi|224589800|ref|NC_000001.10|  8378168 8404227 "ENSG00000162426"       70      1059    26059   0.0406386
Does anybody knows what is the 70, 1059, 26059, 0.0406386 represent?
I know that 0.0406386 is obtained from 1059/26059.
Is it 1059 refer to total number of read aligned to the transcript and 26059 represent the transcript length? How about 70?
Kindly correct me if I'm wrong.
Thanks for any advice.
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