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

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

Hi,

I'm running coveragebed to calculate the number of read count in each transcript of tophat alignment result by using the following command:
Code:
/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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Old 07-01-2011, 05:23 PM   #2
quinlana
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Location: Charlottesville

Join Date: Sep 2008
Posts: 119
Default

If you type "coverageBed -h", the last few lines describe the output format.

Code:
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.
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Old 07-20-2014, 10:46 PM   #3
vineeth.madhavan
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Location: Kochi

Join Date: Feb 2013
Posts: 2
Default Was looking for this detail

Thanks alot , very much helped.
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