Hello,
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.
Sorry for long answer and stupid question. Thank you a lot for your advice. salmon is for transcript alignment.