Question: Cuffdiff merged.gtf to UCSC bed format with gene_id
0
gravatar for ashuseq2015
3.5 years ago by
The Netherlands
ashuseq20150 wrote:

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

rna-seq • 1.4k views
ADD COMMENTlink modified 3.3 years ago by geek_y9.4k • written 3.5 years ago by ashuseq20150

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"

This just shows the first exon of each XLOC. Is that what you want ?

 

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by geek_y9.4k
0
gravatar for geek_y
3.3 years ago by
geek_y9.4k
Barcelona/CRG/London/Imperial
geek_y9.4k wrote:

There is a python script 'dexseq_prepare_annotation.py' in DEXSeq package that can be used get the start and end coordinates of a gene ( gene_id ).

python dexseq_prepare_annotation.py cufflinks.gtf out.gtf
grep aggregate_gene out.gtf > desired_out.gtf

or to a bed file:

grep aggregate_gene out.gtf | sed 's/"//g' | awk -v OFS="\t" '{ print $NF,$4,$5}'​

Output:

XLOC_000001    295    13757
XLOC_000002    31100    43146
ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by geek_y9.4k

This is very informative! thanks

ADD REPLYlink written 2.2 years ago by bioinfo1730
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