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Old 11-24-2015, 11:41 AM   #1
C9r1y
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Location: San Francisco, USA

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Default Estimating PCR duplicates by Counting Reads in BAM file per Read Position

Hello,

I am looking for a tool or script that counts the number of reads in a bam file by position, and takes into account only successfully paired reads. I would like to estimate PCR duplicates when making the (possibly erroneous, I understand!) assumption that reads with the same genomic coordinates are copies.

For example, for the following input:

Chr1:1-500
R1--------------> <---------------R2
R1--------------> <---------------R2
R1--------------> <---------------R2

Chr1:5-505
R1--------------> <---------------R2

Chr1:10-510
R1--------------> <-----------R2
R1--------------> <-----------R2
R1-------------->

I would like to output this information:
Chr1:1-500 3
Chr1:5-505 1
Chr1:10-510 2

Last edited by C9r1y; 11-24-2015 at 01:31 PM.
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Old 11-24-2015, 12:25 PM   #2
blancha
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bedtools multicov with the argument -p.
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Old 11-24-2015, 01:20 PM   #3
C9r1y
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Thanks blancha for the response. However, I would like the position coordinates to be dictated by the read positions, not a bed file of genomic regions.

I would like to estimate the number of pcr duplicates, and will make the assumption that reads that have the exact same start and stop sites are duplicates,
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Old 11-24-2015, 01:59 PM   #4
HESmith
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Then use SAMtools rmdup or Picard MarkDuplicates, since those tools identify duplicates by the same criteria you're using.
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Old 11-24-2015, 02:11 PM   #5
blancha
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Sorry, tired.
How about this one? From Stanford.

http://ngsutils.org/modules/bamutils/pcrdup/

It has an option -counts.

Otherwise, you may just have to find someone to write you a custom script.
I don't know of any tool to give you exactly what you want, although it may exist.
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bam file, deep sequencing, duplicate reads, pcr, read count

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