using featureCounts to have raw counts of the reads

Question

[zizigolu]

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

Answer 1

[Carlo Yague]

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

[zizigolu]

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

[Carlo Yague]

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 :)

[zizigolu]

unfortunately I am not familiar with R,

I used this command

paste file1 file2 | awk '{print $1,$2,$3,$5}'

for merging the file, for example the column one and two from file1 and column 2 from file2 in the same file name file3

am I right?

[zizigolu]

yesssssssssssss the column were separated thank uuuuuuuuuuuuuuuu

[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.

[zizigolu]

thank uuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuu extend to the world, because I have many difficulties in each step but at least in providing the count files you solved my problem kindly.

Answer 2

[zizigolu]

this is another way

cut -f1,7 counts018347.txt > tmp1
cut -f7 counts019035.txt > tmp2
cut -f7 SRR074122.txt > tmp3
cut ...
paste tmp1 tmp2 tmp3 tmp... > summary.txt