Question: How to convert gtf to bed format
0
gravatar for Vasu
15 months ago by
Vasu320
Vasu320 wrote:

I have an annotation gtf file. would like to convert it to bed (BED 12 columns) format. I want the bed file with 12 columns mentioned here [https://genome.ucsc.edu/FAQ/FAQformat.html#format1]

Which means I need the full BED (BED12) that include exon information

thanq

bed gtf • 1.4k views
ADD COMMENTlink written 15 months ago by Vasu320
1

Take a look at gtf2bed from BEDOPS. Information about those extra columns would only be added if you have it in your gtf file.

ADD REPLYlink written 15 months ago by genomax65k

What if I dont have in my gtf file. how can i get 12 column in BED format? BTW tried with BEDOPS but it gave only 6 columns. This means my gtf file doesnt have 12. What i should do now?

ADD REPLYlink modified 15 months ago • written 15 months ago by Vasu320

Depending on what you are trying to do you will need to generate/provide that data, which mainly deals with display of the features.

ADD REPLYlink written 15 months ago by genomax65k

I would like to use that 12 column BED file along with BAM for calculating Transcript integrity number (http://rseqc.sourceforge.net/#tin-py)

ADD REPLYlink written 15 months ago by Vasu320

Have you tried to use the 6 column BED (even though the page you linked seems to indicate a 12-column file)?

ADD REPLYlink written 15 months ago by genomax65k

Sorry for the late reply. Yes, I tried used the 6 column BED file and it gave an output saying - NOTE:input bed must be 12-column

ADD REPLYlink written 15 months ago by Vasu320

See if this BED12 format file works with your data (C: GENCODE v.27 BED 12 file ). It is only a derived file with made up data for display features and your annotation file needs to have 6 columns.

ADD REPLYlink modified 15 months ago • written 15 months ago by genomax65k
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