Question: How to convert gtf to bed format
0
gravatar for Vasu
2.1 years ago by
Vasu420
Vasu420 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 • 2.4k views
ADD COMMENTlink written 2.1 years ago by Vasu420
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 2.1 years ago by genomax78k

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 2.1 years ago • written 2.1 years ago by Vasu420

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 2.1 years ago by genomax78k

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 2.1 years ago by Vasu420

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 2.1 years ago by genomax78k

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 2.1 years ago by Vasu420

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 2.1 years ago • written 2.1 years ago by genomax78k
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