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  • How to merge the annotations

    Hello,

    I have the lincRNA annotation file from UCSC NR*, GENCODE, and other published lincRNA collections. However, i want to merge them into one larger lincRNA collections. what pipeline can do this ?

  • #2
    cat file1 >combinedset.txt
    cat file2 >>combinedset.txt
    cat file3 >>combinedset.txt

    If you need to reformat:
    # Column 1,2,3
    cat file1 | awk -v "OFS=\t" '{ print $1, $2,$3;} >combinedset.txt
    # Column 3,4,5
    cat file2 | awk -v "OFS=\t" '{ print $3, $4,$5;} >>combinedset.txt
    # Column 1, 2,3 : change col 2 from 1 based to 0 based
    cat file3 | awk -v "OFS=\t" '{ print $1, int($2)-1, $3;} >>combinedset.txt

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    • #3
      Originally posted by masylichu View Post
      Hello,

      I have the lincRNA annotation file from UCSC NR*, GENCODE, and other published lincRNA collections. However, i want to merge them into one larger lincRNA collections. what pipeline can do this ?
      can you paste those linCRNA annotation file's weblinks out? i want it either
      Last edited by zinky; 12-05-2012, 11:49 PM.

      Comment


      • #4
        in your merging i assume you might need to check each separate annotation for duplicates between annotations. is that the case?

        if not then 'catting' them together is the right thing to do (assuming you're using a *nix) based system or cygwin in windows. just a dorky note...you can do those cat's in one line:

        Code:
        cat file1 file2 file3 > combinedset.txt
        and you could also do the reformats in one line:

        Code:
        cat <(cut -f1,2,3 file1) <(cut -f3,4,5 file2) <(cut -f1,2,3 file3) > combinedset.txt
        /* Shawn Driscoll, Gene Expression Laboratory, Pfaff
        Salk Institute for Biological Studies, La Jolla, CA, USA */

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        • #5
          Ok, if you end up with something like:

          chr1 1002 9005 linRNA1 . + (BED FORMAT)

          Then you can

          cat combinedfile.bed | sort -k1,1 -k2,2n | uniq >combined.sorted.collapsed.bed

          Then it is sorted by chromosome and only contains unique entries.

          Comment

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