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RNA-seq from Nanopore featureCounts

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.

rna-seq software error r sequencing
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updated by Devon Ryan Devon Ryan • written by v.shapovalova1 • v.shapovalova1

Please use following option to see if it helps since you have long reads :

  -L                  Count long reads such as Nanopore and PacBio reads. Long
                      read counting can only run in one thread and only reads
                      (not read-pairs) can be counted. There is no limitation on
                      the number of 'M' operations allowed in a CIGAR string in
                      long read counting.
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written by GenoMax GenoMax

Hello v.shapovalova1!

We believe that this post does not fit the main topic of this site.

Cross-posted: https://support.bioconductor.org/p/126571/ Lets keep information focused in that BioC question as the developers are active over there.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written by ATpoint ATpoint

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