Anyone know a program or method to create a GC% track for IGV?
I want to convert a bacterial genome sequence into a %GC track to compare depth of coverage with %GC. If there were some code to produce a (for example) wiggle format file from a genome sequence, I could easily display it. Seems like such a program, or at least a module, will already have been written, but I am not finding it.
More details:
I have a couple of Deinococcus radiodurans (~70% GC bacterial genome) TruSeq library data sets sequenced 100x2 PE and aligned to the reference sequence. The average coverage is around 100X, but it is variable and in places very low. I would like to see if the areas of low coverage correlate with the higher GC% areas.
Here is an example window:
Thanks,
--
Phillip
I want to convert a bacterial genome sequence into a %GC track to compare depth of coverage with %GC. If there were some code to produce a (for example) wiggle format file from a genome sequence, I could easily display it. Seems like such a program, or at least a module, will already have been written, but I am not finding it.
More details:
I have a couple of Deinococcus radiodurans (~70% GC bacterial genome) TruSeq library data sets sequenced 100x2 PE and aligned to the reference sequence. The average coverage is around 100X, but it is variable and in places very low. I would like to see if the areas of low coverage correlate with the higher GC% areas.
Here is an example window:
Thanks,
--
Phillip
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