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Old 12-03-2015, 06:30 AM   #1
rnaeye
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Default Coverage plots with inferred fragment sequence from PE reads

Hi!,
I need to make coverage plots/GC bias plots with inferred sequences from Illumina paired-end sequences. Someone here posted that he or she wrote a tool for this purpose. I am wondering if anyone remembers or knows such a tool.

To make it clear: I have 300 bp inserts and I did 2 x 50 bp Illumina sequencing. Thus, middle 200 bp of the fragment is not sequenced. However, I can infer these middle sequences from mapping results to human genome. Itís something I can figure out from SAM file myself, but I think there are available tools that would be more convenient for me to use.

Thank you for the help.
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Old 12-03-2015, 06:47 AM   #2
GenoMax
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Look at the section on "Calculating coverage of the genome" in: http://seqanswers.com/forums/showthread.php?t=58221

You will be using BBMap.
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Old 12-03-2015, 07:46 AM   #3
rnaeye
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Exactly what I was looking for, BBMap. Thanks GenoMax!
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coverage, gc bias, illumina, paired end mapping

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