Question: How can I convert from bed to bed12 format?
0
gravatar for Sharon
11 months ago by
Sharon420
Sharon420 wrote:

Hi Everyone

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

Thanks

bed12 bed • 682 views
ADD COMMENTlink modified 11 months ago by Hussain Ather910 • written 11 months ago by Sharon420
2

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

ADD REPLYlink modified 11 months ago • written 11 months ago by Bastien Hervé3.9k

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

ADD REPLYlink written 11 months ago by Hussain Ather910

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 :)

ADD REPLYlink written 11 months ago by Sharon420

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 :)

ADD REPLYlink written 11 months ago by Bastien Hervé3.9k

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 :)

ADD REPLYlink modified 11 months ago • written 11 months ago by Sharon420

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

ADD REPLYlink written 11 months ago by Bastien Hervé3.9k

I know that it is outdated.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.

ADD REPLYlink written 11 months ago by Sharon420
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