User: Teeps

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Teeps0
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Posts by Teeps

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Pull out sequences between ranges?
... Hi everyone. Simple question but I'm new to bioconductor. I have a DNAString (myDNAStringSet) and a GRanges object made from a BED file (myGRangesObject) so I can find the sequences of the exons in myDNAStringSet using: getSeq(myDNAStringSet, myGRangesObject). How could I pull out user defined sec ...
getsequence written 4 months ago by Teeps0 • updated 4 months ago by roxys91500
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Comment: C: Annotating a sequence, new to bioconductor
... Thank you for the help. I worked on making a BSGenome object for a bit but it was a bit beyond me right now. I found I could pull it up by, after making sure all the names were the same, using "getSeq(myDNAStringSet, myGRangesObject). I can pull out individual genes marked on the BED file I used for ...
written 4 months ago by Teeps0
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Comment: C: Annotating a sequence, new to bioconductor
... Hi, thank you for the help and sorry for the late reply, I had an emergency come up and didn’t have time for BioC this last week.  I’ll try to clarify a bit more. I can make a GRange object with the BED file like you showed, but it’s not referencing a genome. If I do seqinfo(x) under “genome” it’s ...
written 5 months ago by Teeps0
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Annotating a sequence, new to bioconductor
... New to BioC, just trying to learn. I’ve got a sequence file (FASTA) and an annotation file (BED) with the various ranges of genes and other features. I would like to use the BED file to annotate my sequence, and then be able to pull out portions of the sequence not found in the BE file (eg, 200 bp n ...
annotate written 5 months ago by Teeps0 • updated 5 months ago by James W. MacDonald49k

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