Rsubread Read Bam and filter reads by TAG field
0
0
Entering edit mode
@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)
Rsubread featurecounts featurerequest • 1.4k views
ADD COMMENT
0
Entering edit mode

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

Login before adding your answer.

Traffic: 758 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6