featurecounts

Question

[sehriban.buyukkilic]

Hi everyone, I'm doing featurecounts for my RNA-seq data. But there is something with result. Can anyone tell me what is wrong with it?

/truba/home/sbuyukkilic/fastqc_tool/subread-1.5.3-Linux-x86_64/bin/featureCounts -a /truba/home/sbuyukkilic/files/gencode.v42.annotation.gtf -o /truba/home/sbuyukkilic/fastqc_tool/readCount/SRR22016667_2_counts.txt /truba/home/sbuyukkilic/fastqc_tool/Analysis_test/align/SRR22016667_2.fastq.gzAligned.out.sam

when I running this command for featurecounts I got result of below.

Answer 1

[ATpoint]

Nothing is wrong. You simple have to skip the first line when reading into R (or anything), use read.delim(x, header=TRUE, skip=1).