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alessandro.pastore
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20
@alessandropastore-10879
Last seen 6.0 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)
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 infeatureCounts
what you are after?