Bundled data for hg38/ensembl 88

[ahy1221]

Hi ,
I was wondering is that possible to use fishhook on hg38/ensembl88 based mutation ? Since the GDC is providing new called TCGA mutations on hg38, it would be better to provide tutorial about how to prepare the CDS reference data(cds definition file) of fishhook

Yao

[mskilab]

Sure can update the tutorial with hg38 info but nothing fundamentally changes if you use a different genome (including human vs. mouse vs. yeast). You can get the cds doing rtracklayer::import on the transcript .gff file (e.g. hg38 build from GENCODE) and then subset on the intervals that have type == 'CDS'. e.g. rtracklayer::import(gff.url) %Q% (type == 'CDS') The covariates (e.g. replication timing, GC content, chromatin marks) you will have to import or compute from the matched genome, but that's just a matter of finding the appropriate bed or wig files. You would need to do this for a different tumor type (e.g. lung) as well.

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On Mon, Nov 5, 2018 at 5:38 AM Yao He ***@***.***> wrote: Hi , I was wondering is that possible to use fishhook on hg38/ensembl88 based mutation ? Since the GDC is providing new called TCGA mutations on hg38, it would be better to provide tutorial about how to prepare the CDS reference data(cds definition file) of fishhook Yao — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#4>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AL-0kY0l_zB3iYeqetz7u1q-oi5wRGwbks5usBUggaJpZM4YOLP7> .

[ahy1221]

Thank you very much ! Is that a list of which bed files you are using or importing from hg19/UCSC ?