How to convert gtf to bed format
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
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Take a look at gtf2bed from BEDOPS. Information about those extra columns would only be added if you have it in your gtf file.
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?
Depending on what you are trying to do you will need to generate/provide that data, which mainly deals with display of the features.
I would like to use that 12 column BED file along with BAM for calculating Transcript integrity number (http://rseqc.sourceforge.net/#tin-py)
Have you tried to use the 6 column BED (even though the page you linked seems to indicate a 12-column file)?
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
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.