Question

Extract gene coordinates from GTF

3

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9.9 years ago

int11ap1 ▴ 470

Hello,

I have a GTF file with only exon features. There's a way to extract the gene coordinates? Or should I write a script?

INPUT: GTF file.
OUTPUT: the gene coordinates, whatever the format is.

Thanks.

coordinates gtf • 14k views

ADD COMMENT • link updated 2.5 years ago by Ram 43k • written 9.9 years ago by int11ap1 ▴ 470

0

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Please make it more clear by showing your Input file and desired output

ADD REPLY • link 9.9 years ago by ancient_learner ▴ 680

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Done, I cannot be more clear.

ADD REPLY • link 9.9 years ago by int11ap1 ▴ 470

Ram · Answer 1 · 2014-06-13

7

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9.9 years ago

Devon Ryan 104k

The question becomes exactly what you want in terms of coordinates for a gene. I'm guessing that you just want the 5' most and 3' most position along with the strand an chromosome, but perhaps you have something else in mind.

Presuming you do want what I mentioned, you could easily do this in R with GenomicFeatures.

library(GenomicFeatures)
txdb <- makeTranscriptDbFromGFF("some_file.gtf", format="gtf")
genes <- genes(txdb)
write.table(as.data.frame(genes)[,-4], file="Just_genes.txt", colnames=F, sep="\t")

The -4 just removes the width column.

ADD COMMENT • link updated 4.3 years ago by Ram 43k • written 9.9 years ago by Devon Ryan 104k

4

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Years later, I would like to make a little update, to maybe save someone 2 minutes: Since some of the last updates the function makeTranscriptDbFromGFF of the package GenomicFeatures is now called makeTxDbFromGFF.

ADD REPLY • link 5.5 years ago by caggtaagtat ★ 1.9k

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I'm getting this error

Error in write.table(as.data.frame(genes)[, -4], file = "Just_genes.txt",  :

unused argument (colnames = F)

ADD REPLY • link 7.0 years ago by 1769mkc ★ 1.2k

2

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Try again with

write.table(as.data.frame(genes)[,-4], file="Just_genes.txt", col.names=F, sep="\t")

ADD REPLY • link 7.0 years ago by thomas musielak ▴ 20

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Hi Devon, How would you get the gene description along with the gene coordinates using a similar script as you presented. Thanks

Dave

ADD REPLY • link 4.8 years ago by dklinkebiel • 0

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Hi @Devon Ryan, i have a gff file in this format:

chr11   Gnomon  gene    24482947    24484914    .   -   .   ID=gene26171;Name=LOC103966979;Name=gene26171
chr11   Gnomon  mRNA    24482947    24484914    .   -   .   Parent=gene26171;ID=rna33198
chr11   Gnomon  five_prime_UTR  24484810    24484914    .   -   .   ID=five_prime_UTR:rna33198:1;Parent=rna33198
chr11   Gnomon  start_codon 24484807    24484809    .   -   0   ID=start_codon:rna33198:1;Parent=rna33198
chr11   Gnomon  exon    24484587    24484914    .   -   .   ID=exon:rna33198:1;Parent=rna33198
chr11   Gnomon  exon    24484138    24484445    .   -   .   ID=exon:rna33198:2;Parent=rna33198
chr11   Gnomon  exon    24482947    24483988    .   -   .   ID=exon:rna33198:3;Parent=rna33198
chr11   Gnomon  CDS 24484587    24484809    .   -   0   Parent=rna33198;ID=CDS:rna33198:1
chr11   Gnomon  CDS 24484138    24484445    .   -   2   Parent=rna33198;ID=CDS:rna33198:2
chr11   Gnomon  CDS 24483413    24483988    .   -   0   Parent=rna33198;ID=CDS:rna33198:3
chr11   Gnomon  gene    21571688    21575140    .   -   .   Name=LOC103939934;ID=gene39438;Name=gene39438
chr11   Gnomon  mRNA    21571688    21575140    .   -   .   ID=rna49862;Parent=gene39438
chr11   Gnomon  five_prime_UTR  21575032    21575140    .   -   .   ID=five_prime_UTR:rna49862:1;Parent=rna49862
chr11   Gnomon  five_prime_UTR  21574449    21574449    .   -   .   Parent=rna49862;ID=five_prime_UTR:rna49862:2
chr11   Gnomon  exon    21575032    21575140    .   -   .   ID=exon:rna49862:1;Parent=rna49862
chr11   Gnomon  exon    21574389    21574449    .   -   .   Parent=rna49862;ID=exon:rna49862:2
chr11   Gnomon  exon    21572908    21572989    .   -   .   ID=exon:rna49862:3;Parent=rna49862
chr11   Gnomon  exon    21572290    21572417    .   -   .   ID=exon:rna49862:4;Parent=rna49862
chr11   Gnomon  exon    21571688    21572198    .   -   .   ID=exon:rna49862:5;Parent=rna49862
chr11   Gnomon  start_codon 21574446    21574448    .   -   0   Parent=rna49862;ID=start_codon:rna49862:1
chr11   Gnomon  CDS 21574389    21574448    .   -   0   ID=CDS:rna49862:1;Parent=rna49862
chr11   Gnomon  CDS 21572908    21572989    .   -   0   Parent=rna49862;ID=CDS:rna49862:2
chr11   Gnomon  CDS 21572290    21572417    .   -   2   Parent=rna49862;ID=CDS:rna49862:3
chr11   Gnomon  CDS 21571866    21572198    .   -   0   Parent=rna49862;ID=CDS:rna49862:4

and i have a genes ID:

LOC103966979
LOC103939934

and i want to extract there transcripts info in this format:

chr11   Gnomon  mRNA    24482947    24484914    .   -   .   ID=LOC103966979
chr11   Gnomon  five_prime_UTR  24484810    24484914    .   -   .   ID=five_prime_UTR:rna33198:1;Parent=LOC103966979
chr11   Gnomon  start_codon 24484807    24484809    .   -   0   ID=start_codon:rna33198:1;Parent=LOC103966979
chr11   Gnomon  CDS 24484587    24484809    .   -   0   ID=CDS:rna33198:1;Parent=LOC103966979
chr11   Gnomon  CDS 24484138    24484445    .   -   2   ID=CDS:rna33198:2;Parent=LOC103966979
chr11   Gnomon  CDS 24483413    24483988    .   -   0   ID=CDS:rna33198:3;Parent=LOC103966979
chr11   Gnomon  mRNA    21571688    21575140    .   -   .   ID=LOC103939934
chr11   Gnomon  five_prime_UTR  21575032    21575140    .   -   .   ID=five_prime_UTR:rna49862:1;Parent=LOC103939934
chr11   Gnomon  five_prime_UTR  21574449    21574449    .   -   .   ID=five_prime_UTR:rna49862:2;Parent=LOC103939934
chr11   Gnomon  start_codon 21574446    21574448    .   -   0   ID=start_codon:rna49862:1;Parent=LOC103939934
chr11   Gnomon  CDS 21574389    21574448    .   -   0   ID=CDS:rna49862:1;Parent=LOC103939934
chr11   Gnomon  CDS 21572908    21572989    .   -   0   ID=CDS:rna49862:2;Parent=LOC103939934
chr11   Gnomon  CDS 21572290    21572417    .   -   2   ID=CDS:rna49862:3;Parent=LOC103939934
chr11   Gnomon  CDS 21571866    21572198    .   -   0   ID=CDS:rna49862:4;Parent=LOC103939934

thanks for adivice.

ADD REPLY • link 3.8 years ago by Kurban ▴ 230

0

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You'd need to script something.

ADD REPLY • link 3.7 years ago by Devon Ryan 104k

Ram · Answer 2 · 2015-02-20

6

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9.2 years ago

Alex Reynolds 35k

Using gtf2bed:

$ gtf2bed < foo.gtf | cut -f1-3 > foo_coords.bed3

If you want strand information:

$ gtf2bed < foo.gtf | cut -f1-6 > foo_coords.bed6

ADD COMMENT • link updated 4.5 years ago by Ram 43k • written 9.2 years ago by Alex Reynolds 35k

score 5 · Answer 3 · 2014-06-13

using awk and sqlite:

curl -sL "https://rseqflow.googlecode.com/files/mouse_refseq_anno.gtf"   |\
awk -F '    ' 'BEGIN {printf("create temp table T(chrom,start,end,gene); begin transaction;\n");} $3=="exon" {n=split($9,a,/[ ;]+/);for(i=1;i+1< n;i++) if(a[i]=="gene_id") printf("insert into T(chrom,start,end,gene) values (\"%s\",%s,%s,%s);\n",$1,$4,$5,a[i+1]);} END {printf("commit; select chrom,gene,min(start),max(end) from T group by chrom,gene;\n");}' |\
sqlite3 tmp.db
(...)
chrY|Rbm31y|12688110|17402718
chrY|Rbmy1a1|2830680|3783271
chrY|Sly|55213720|75222053