User: teresati

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teresati10
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Posts by teresati

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generate table of counts with strand-specific paired-end RNA-seq data
... Dear All, I have strand-specific paired-end RNA-seq data, and I am attempting to generate a table of reads counts. I wanted to ask if the following steps are correct: 1. load separately bam files with BamFile function and specify asMates=TRUE for paired-end reads bamflU1 <- BamFile("PATH/U1.b ...
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plotting correlation between samples
... Dear all, I would like to plot the correlation between my samples. I have a matrix with genes in rows and samples in columns, and for each gene a logCPM normalized values. If I want to look at the correlation between 2 samples I get an Error: x <- as.data.frame(t(log.cpm.norm[,1])) y <- a ...
correlation written 21 months ago by teresati10 • updated 21 months ago by Aaron Lun21k
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Answer: A: how to renameSeqlevels-GenomicAlignments
... Apologies, I have loaded a bam file (mapped on transcript) and a gff file: >library(GenomicAlignments) >bamfileS1 <-list.files("/path/to/bam/S1.bam", pattern="bam$", full=TRUE) GAlignments object seqnames ...
written 22 months ago by teresati10
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how to renameSeqlevels-GenomicAlignments
... Dear all,   I would like to ask if it is possible to change the seqnames of a bam file object, giving a vector of character to the function renameSeqlevels. This is because in order to use the fuction summarizeOverlap or count/find, the seqnames have to match. From the bamfile object below, I have ...
annotation renameseqlevels galignments bamfileobject written 22 months ago by teresati10

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