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Old 10-30-2015, 03:57 AM   #1
Ashu123
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Default 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
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Old 10-30-2015, 05:29 AM   #2
Ashu123
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Location: Holland

Join Date: Oct 2015
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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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