Hi everyone,
I am interested in determining G+C rich regions in a whole genome sequence as well as identifying possible CpG Islands.
Can anyone recommend their favourite resources for either of these tasks?
So far, for G+C content, I have tried Picard's CollectGCBiasMetrics (doesn't give me the right info) and GATK's GCContentByInterval walker (gives me a persistent error message) and I am just in the process of trying to run GCProfile.
If anyone has used the GCContentByInterval walker could you perhaps give me an example of your code so that I might be able to compare and see where mine is going wrong.
For CpG Islands I have found 'CpGIslands' but have not yet tried it.
I am new to programming so any help would be much appreciated.
Many thanks
Helen
I am interested in determining G+C rich regions in a whole genome sequence as well as identifying possible CpG Islands.
Can anyone recommend their favourite resources for either of these tasks?
So far, for G+C content, I have tried Picard's CollectGCBiasMetrics (doesn't give me the right info) and GATK's GCContentByInterval walker (gives me a persistent error message) and I am just in the process of trying to run GCProfile.
If anyone has used the GCContentByInterval walker could you perhaps give me an example of your code so that I might be able to compare and see where mine is going wrong.
For CpG Islands I have found 'CpGIslands' but have not yet tried it.
I am new to programming so any help would be much appreciated.
Many thanks
Helen
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