How can I convert from bed to bed12 format?

Question

[Sharon]

Hi Everyone

Any hint on how can I convert from bed to bed12 format?

Thanks

[Bastien Hervé]

What kind of bed do you have ?

Do you have more informations about your data ?

What are you trying to achieve ?

If you have a bed with only 3 columns (chrom, start, end) , you can't transform directly your bed to bed12, you will need a gtf/gff file.

See here BED format : https://genome.ucsc.edu/FAQ/FAQformat.html#format1

[Hussain Ather]

You need more information than what's generally provided in the bed file. What programming language would you like to use?

[Sharon]

I meant bed6 to bed12. I need this to use lnscore, but I find another way. I used -G in cufflinks to get transcripts.gtf then converted from here. Thanks a lot guys :)

[Bastien Hervé]

I would just say that I read that stringTie should be use rather than Cufflinks, here by example : which file I can use for cufflinks from the aligner STAR But i'm not 100% sure so I let you with my doubt :)

[Sharon]

it was causing me the same problem, showing the ID STR same as CUFF id. When I used -G i got the transcripts names itseld not just CUFF or STR. But the link you showed is nice, as I can now use star instead of my tophat bams :) Thanks so much Bastien :)

[Bastien Hervé]

The association TopHat/Cufflinks is from 2012 and need to be bannished. The association HISAT/stringTie is much more relevant now https://www.nature.com/articles/nprot.2016.095

[Sharon]

I know that it is outdated. But long story here ! I usually use salmon or star and edgerR or deseq2 fron RNA expression but testing the water for slncky and lncscore some lncrna tools. so I am checking how they work with some old bams we have. Once I check how they work, I can move to star or anything else on the new data.

Answer 1

[ashotmarg2004]

It's worth checking out this tool: https://github.com/muhligs/bed6ToBed12