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User: andreag1987

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Posts by andreag1987

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Answer: A: issue retrieving metadata after psetdiff function
... By the way I found a solution, I edited the psetdiff() methods adding the following line: mcols(ansGRanges)<-rep(mcols(x),elementNROWS(ansRanges)) Here the code with the added line: setMethod("psetdiff", c("GRanges", "GRangesList"), function(x, y, ignore.strand=FALSE) { ...
written 13 months ago by andreag19870
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issue retrieving metadata after psetdiff function
... Hello, I am trying to fetch promoter regions that don't overlap with cds. This is what my code looks like: phy<-makeTxDbFromGRanges(phy) GR <- cds(phy,columns=c("GENEID","TXID","CDSNAME","CDSID")) indexFa(file.choose()) #select the fasta file fasta<-file.choose() phy.fasta<-FaFile(f ...
granges grangeslist written 13 months ago by andreag19870
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Answer: A: Rsamtools ScanFA error
... Dear Prof.Morgan thank you very much for your help! I solved the problem, here the solution I found: promoter_seqs<-GRangesList(   restrict(promoter_seqs[seqnames(promoter_seqs)=="1"],start = 1,end = 3479187),   restrict(promoter_seqs[seqnames(promoter_seqs)=="2"],start = 1,end = 2697374),   rest ...
written 14 months ago by andreag19870
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Rsamtools ScanFA error
...   I am trying to fetch promoter sequences from a bacterial genome, retrieving only those sequences that don't fall into cds. I think the problem is that some sequences fall out of the FASTA sequences (2 chromosomes, 2 plasmids) that are not recognized as circular giving me an ...
rsamtools written 14 months ago by andreag19870

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