FeatureCounts Number of Reads

Question

[santos48]

Hi everyone, I have over 4000 human Rna-seq data reading by nanopore Minion, I merged all files with the 'cat' command. I am using featureCounts for counting features of aligned Rna-Seq. After the featureCounts when I control with multiQC report I saw the number of reads 4k but it should be over the million.

Should I merge after aligned against the ref genome before start analysis?

[ATpoint]

I have over 4000 human Rna-seq data reading by nanopore Minion

What does that mean? You have 4000 files, or samples? Please explain.

[santos48]

4000 fastq files

[WouterDeCoster]

How did you merge them with cat? Can you show your command?

[santos48]

cat /*.fastq >all.fastq

[ATpoint]

If this is the precise command then this has two problems:

a) / means the root folder where most likely these files are not stored, you probably meant to use ./ which means current directory, and

b) it might be that the newly created file gets concatenated to itself, better:

find . -maxdepth 1 -name "*.fastq" | xargs cat > new.fastq