I have RNA-seq reads from Nanopore(kit RNA002, U-based fastq), I aligned them with minimap2 and tried to count with featureCounts. The reference was transcriptome from https://www.gencodegenes.org/human/. my command was
fc<- Rsubread::featureCounts(files="aln.bam",annot.inbuilt="hg38",isLongRead="True") Process BAM file aln.bam... || || Single-end reads are included. || || Total alignments : 2081002 || || **Successfully assigned alignments : 0 (0.0%)** || || Running time : 0.26 minutes **Warning message: In paste("readSummary", ann, files_C, fout, as.numeric(isPairedEnd), : NAs introduced by coercion**
I checked my bam file and have such a statistics:
SN raw total sequences: 632940 SN filtered sequences: 0 SN sequences: 632940 SN is sorted: 1 SN 1st fragments: 632940 SN last fragments: 0 SN reads mapped: 609258 SN reads mapped and paired: 0 # paired-end technology bit set + both mates mapped SN reads unmapped: 23682
What could it be?
A lot of thanks.