Rsubread Read Bam and filter reads by TAG field

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alessandro.pastore ▴ 20

@alessandropastore-10879

Last seen 6.1 years ago

I have multi samples BAM files (from 10x Experiments). My aim is to count reads on genomic region. I am using the

tagFilter parameter of ScanBamParam with summarizeOverlaps to import each single cells. It would be nice if also something like this would be possible with featurecounts() .

Thanks!

Filter <- list(1_cell.barcode)
names(Filter) <- "CB"

BamParam <- ScanBamParam(what=scanBamWhat(), tagFilter = Filter )

bamfile <- BamFile(file.names, yieldSize=5000)

summarizeOverlaps(GrangeList, bamfile, param = BamParam)

Rsubread featurecounts featurerequest • 1.5k views

ADD COMMENT • link 6.9 years ago alessandro.pastore ▴ 20

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Sorry for my slow response. However I am not quite sure what feature you request here. As far as I know reads from each single cell are often organized as a read group in a bam file. Is the 'byReadGroup' option in featureCounts what you are after?

ADD REPLY • link 6.9 years ago Wei Shi ★ 3.6k

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