How can I convert from bed to bed12 format?
Hi Everyone
Any hint on how can I convert from bed to bed12 format?
Thanks
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ashotmarg2004 •
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Sharon
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Sharon
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It's worth checking out this tool: https://github.com/muhligs/bed6ToBed12
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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
You need more information than what's generally provided in the bed file. What programming language would you like to use?
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 :)
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 :)
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 :)
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
I know that it is outdated.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.