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

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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.
edge is offline   Reply With Quote
Old 07-01-2011, 05:23 PM   #2
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If you type "coverageBed -h", the last few lines describe the output format.

Default Output:  
	 After each entry in B, reports: 
	   1) The number of features in A that overlapped the B interval.
	   2) The number of bases in B that had non-zero coverage.
	   3) The length of the entry in B.
	   4) The fraction of bases in B that had non-zero coverage.
quinlana is offline   Reply With Quote
Old 07-20-2014, 10:46 PM   #3
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Default Was looking for this detail

Thanks alot , very much helped.
vineeth.madhavan is offline   Reply With Quote

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