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  • Ashu123
    Junior Member
    • Oct 2015
    • 2
    #1

    Cuffdiff merged.gtf to UCSC bed format with gene_id

    Cuffmerg merged.gtf to UCSC bed format with gene_id

    Dear all,
    I have the following format from Cufflinks/cuffmerge, I would like to convert to a bed format, by merging the transcripts (transcript_id). in other words, I would like to have the files converted to bed file with gene_id only.

    the input is:

    chr1 Cufflinks exon 295 1580 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; oId "CUFF.4.1"; tss_id "TSS1";
    chr1 Cufflinks exon 3851 4424 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "2"; oId "CUFF.4.1"; tss_id "TSS1";
    chr1 Cufflinks exon 7276 7377 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "3"; oId "CUFF.4.1"; tss_id "TSS1";
    chr1 Cufflinks exon 8527 8720 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "4"; oId "CUFF.4.1"; tss_id "TSS1";
    chr1 Cufflinks exon 11556 13757 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "5"; oId "CUFF.4.1"; tss_id "TSS1";
    chr1 Cufflinks exon 1518 1557 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "1"; oId "CUFF.4.2"; tss_id "TSS2";
    chr1 Cufflinks exon 3851 4424 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "2"; oId "CUFF.4.2"; tss_id "TSS2";
    chr1 Cufflinks exon 7276 7377 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "3"; oId "CUFF.4.2"; tss_id "TSS2";
    chr1 Cufflinks exon 8527 8720 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "4"; oId "CUFF.4.2"; tss_id "TSS2";
    chr1 Cufflinks exon 11556 13757 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "5"; oId "CUFF.4.2"; tss_id "TSS2";
    chr1 Cufflinks exon 1746 2079 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000003"; exon_number "1"; oId "CUFF.4.3"; tss_id "TSS3";
    chr1 Cufflinks exon 3851 4424 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000003"; exon_number "2"; oId "CUFF.4.3"; tss_id "TSS3";
    chr1 Cufflinks exon 7276 7377 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000003"; exon_number "3"; oId "CUFF.4.3"; tss_id "TSS3";
    chr1 Cufflinks exon 8527 8720 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000003"; exon_number "4"; oId "CUFF.4.3"; tss_id "TSS3";
    chr1 Cufflinks exon 11556 13757 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000003"; exon_number "5"; oId "CUFF.4.3"; tss_id "TSS3";
    chr1 Cufflinks exon 31100 33382 . - . gene_id "XLOC_000002"; transcript_id "TCONS_00000004"; exon_number "1"; oId "CUFF.5.1"; tss_id "TSS4";
    chr1 Cufflinks exon 36218 36411 . - . gene_id "XLOC_000002"; transcript_id "TCONS_00000004"; exon_number "2"; oId "CUFF.5.1"; tss_id "TSS4";
    chr1 Cufflinks exon 37561 37662 . - . gene_id "XLOC_000002"; transcript_id "TCONS_00000004"; exon_number "3"; oId "CUFF.5.1"; tss_id "TSS4";
    chr1 Cufflinks exon 40514 41087 . - . gene_id "XLOC_000002"; transcript_id "TCONS_00000004"; exon_number "4"; oId "CUFF.5.1"; tss_id "TSS4";
    chr1 Cufflinks exon 42859 43146 . - . gene_id "XLOC_000002"; transcript_id "TCONS_00000004"; exon_number "5"; oId "CUFF.5.1"; tss_id "TSS4";
    chr1 Cufflinks exon 31100 33382 . - . gene_id "XLOC_000002"; transcript_id "TCONS_00000005"; exon_number "1"; oId "CUFF.5.3"; tss_id "TSS5";

    the output I would like to have is:


    chr1 Cufflinks exon 295 1580 . + . gene_id "XLOC_000001"
    chr1 Cufflinks exon 31100 33382 . - . gene_id "XLOC_000002"

    with the chr start (column 4) and chr end (column 5), representing start and end of all other isofoms or longest.

    Thank you very much for your help!

    Regards,
    Ashu
    Tags: None
    • Ashu123
      Junior Member
      • Oct 2015
      • 2
      #2
      Deal All,
      If you also know another link, where this has been discussed and I missed, please let me know.
      Thank you in advance!
      Ashu

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