FeatureCounts Number of Reads
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?
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ATpoint
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santos48 •
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santos48 •
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What does that mean? You have 4000 files, or samples? Please explain.
4000 fastq files
How did you merge them with cat? Can you show your command?
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, andb) it might be that the newly created file gets concatenated to itself, better: