sorry friends,
using
[izadi@lbox161 bin]$ featureCounts -t exon -g gene_id -a genes.gtf -o counts.txt accepted_hits.bam
command, I have a counts.txt.summary in the first row I see like this
#Program:featureCounts v1.4.6-p5; Command:"featureCounts" "-t" "exon" "-g" "gene_id" "-a" "genes.gtf" "-o" "counts.txt" "accepted_hits.bam"
Geneid Chr Start End Strand Length accepted_hits.bam
AT1G01010 1;1;1;1;1;1 3631;3996;4486;4706;5174;5439 3913;4276;4605;5095;5326;5899 +;+;+;+;+;+ 1688 31
I need the raw counts, RPKM and VST files...then how i extract the raw counts file as an input for DEseq package to get RPKM and VST files??
thank you
You need to run featureCounts on all your libraries. Then you extract and merge the first and last columns of your counts.txt.summary files. It shoud looks like this:
GeID library_1 library_2 library_3 library_4
AT1G01010 31 50 24 21
•
written
by
Carlo Yague
sorry, with the below command I extracted the column one and the last column this is like below, do you think I should separate the columns because they are too close to each other
cat counts.txt | awk '{ print $1 $7 }' > file.txt2
#"-g"
Geneid accepted_hits.bam
AT1G01010 31
AT1G01020 153
AT1G01030 10
AT1G01040 88
AT1G0104 60
AT1G01050228
try to add tabulations:
cat counts.txt | awk '{ print $1 "\t" $7 }' > file.txt2
But it might be easier to do this with R if you are familiar with it :)
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written
by
Carlo Yague
Hi, sorry for the late answer. If your command works, then its right ! But it is probably not the most efficient solution : You first paste all your columns then extract the columns you need. It would be more efficient to do something like this:
paste <(cut -f1,7 file1) <(cut -f7 file2) <(cut -f7 file3) <(cut -f7 file4) > summary.txt
That way you first extract the columns you need, then merge them into one file.
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written
by
Carlo Yague
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