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  • why doesn't this linux command work for me?

    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

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

    Comment


    • #3
      Richard,
      I still got the same output---just merged the two files with ID of each kept.

      Comment


      • #4
        Perhaps tab isn't the default delimiter for paste on your system? Maybe then

        Code:
        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).

        Comment


        • #5
          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.

          Comment

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