why doesn't this linux command work for me?

[wmseq]

Hi every one,
I'd like merging the following two HTSeq-count outputs using the following command--- paste UHR1_htseq-count.out UHR2_htseq-count.out brain1_htseq-
count.out brain2_htseq-count.out | awk -F "\t" '{print
$1"\t"$2"\t"$4"\t"$6"\t"$8 }' > All_htseqCounts.txt


head UHR1_htseq-count.out
A1BG 67
A1CF 31
A2BP 3

head UHR2_htseq-count.out
A1BG 67
A1CF 39
A2BP 1
-----
I got the following output.

A1BG 67 A1BG 67
A1CF 31 A1CF 39
A2BP 3 A2BP 1
----
In fact I want to get the folloing one.

A1BG 67 67
A1CF 31 39
A2BP 3 1

Is there any one who know what is wrong with the command?

Thanks a lot?

Richard

[Richard Finney]

paste file1 file2 | awk '{print $1" "$2" "$4}'

[wmseq]

Richard,
I still got the same output---just merged the two files with ID of each kept.

[dpryan]

Perhaps tab isn't the default delimiter for paste on your system? Maybe then

paste -d "\t" file1 file2 | awk '{OFS="\t"; print $1,$2,$4}'

Alternatively, perhaps the files aren't actually tab delimited to begin with (try running "cut -f 1" on one of them).

[Richard Finney]

Are you using bash?
Run this command ...

set | grep FS

Also, look at the actual bytes ...
od -x UHR1_htseq-count.out | head

to see if that's a space or a tab.