coverting gtf to bed

Question

[zizigolu]

Hi,

Based on previous biostars post about converting gtf to bed, I converted my gtf file to bed like below

gtf2bed < merged.gtf > merged.bed

I also tried

gtf2bed < merged.gtf > unsorted-foo.gtf.bed

But unreadable anyway. But the resulted file is unreadable by kate or all, do you know why please?

[GenoMax]

I assume you are getting something in the converted file since you say it is unreadable? Can you post a few lines from the top of the converted file?

[zizigolu]

but i cant open the converted file and i tried to open the file with kate the file was empty

[GenoMax]

Did you look at merged.gtf to make sure that looked reasonable since the conversion is not working?

[zizigolu]

thank you

this is the first column of merged gtf

1    Cufflinks    exon    3631    3913    .    +    .    gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; gene_name "NAC001"; oId "AT1G01010.1"; nearest_ref "AT1G01010.1"; class_code "="; tss_id

[GenoMax]

If you just need a minimal bed file you could just do following. Record separator is a space in the command below. Replace it with a \t (e.g. -F "\t"), if that is what is in your file.

$ awk -F " " 'BEGIN {OFS="\t"}{print $1,$4,$5}' merged.gtf > merged.bed

[zizigolu]

thank you so much,

first I was working with prokaryotes then I used bowties as an aligner and downstream tool, finally this is the first row of my bed file

YAL001C    0    31    SRR1944914.13670510    42    +

but now I am working with eukaryotes then I used tophat as an aligner and cufflinks package that I have finally a merged.gtf by cuffdiff that the first row

1    Cufflinks    exon    3631    3913    .    +    .    gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; gene_name "NAC001"; oId "AT1G01010.1"; nearest_ref "AT1G01010.1"; class_code "="; tss_id

my main purpose of these analysis is having how many reads are being mapped on a gene and in which distance...then gene_name in merged.gtf showing the times genes repeating as the number of reads are being mapped also columns 4th and 5th in merged.gtf showing the distances these reads are mapped..anyway I am using biophysconnector package that needs a bed file, then I thought to convert my gtf.file to bed