Question: Rsubread : featureCounts PEReadsReordering=TRUE deletes unpaired reads?
4.0 years ago by
Ryan C. Thompson ♦ 6.1k
The Scripps Research Institute, La Jolla, CA
Ryan C. Thompson ♦ 6.1k wrote:
Hello, I am using the featureCounts function in Rsubread to count RNA-seq reads. Since my BAM files are coordinate-sorted paired-end, I am using "isPairedEnd=TRUE" and "PEReadsReordering=TRUE". When I run my script, I see the following in the output: Process /gpfs/home/rcthomps/Projects/cyno/tophat_results/R77_CN7314_P4 ... Resort the input file ... 2718714 unpaired reads were ignored in reordering. Total number of fragments is : 1653582 Number of successfully assigned fragments is : 1529491 (92.5%) Running time : 3.39 minutes In particular, I am worried about the line "2718714 unpaired reads were ignored in reordering." The documentation for PEReadsReordering doesn't say anything about discarding unpaired reads, so I'm wondering whether this is intended behavior, and whether there is a way around this? If I sort my bam files by name so that pairs are adjacent in the file, will subread still discard the unpaired ones, or will it count all of them? -Ryan Thompson
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