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dieterich-lab / DCC

DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates.
https://dieterichlab.org/software/
GNU General Public License v3.0
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read support for oRNA candidates #75

Closed harperfauni closed 2 years ago

harperfauni commented 4 years ago

Hello,

I was just wondering if the read support for the circular RNA candidates are 0-based or 1-based coordinates. It seems that the read support are obtained from 1-based coordinates while other oRNA discovery tools such as CircExplorer2 and circRNA_finder are 0-based.

My question: Is it possible to obtain read support from 0-based coordinates?

Thanks!

Best,

Harper

tjakobi commented 4 years ago

Hi @harperfauni,

DCC is based on output from the STAR read mapper. The positions that are contained the chimeric output files are 1-based, therefore DCC in general is also 1-based.

However, if you require 0-based numbers, you may use sed or similar command line tools to convert the positions accordingly.

Cheers, Tobias

harperfauni commented 4 years ago

Hello Tobias,

Thank you for answering promptly! I was just concerned that even if I adjust the coordinates to 0-based that the read support would still be 1-based. Do you think that if I adjust the positions on the chimeric junction files then the oRNA read support would also be adjusted?

Best, Harper

harperfauni commented 4 years ago

Is it possible to alter some of the scripts to pull the support reads based on 0-based coordinates?

tjakobi commented 4 years ago

Dear @harperfauni,

just so that we are on the same page. You would like to extract the reads that have been mapped to the BSJ per circRNA and would like to have those read mapping coordinates on a 0-based scale?

You shouldn't modify the chimeric.junction.out files of STAR, rather you may modify the DCC results. You can than extract BSJ reads i.e. with bedtools from the BAM files produced by STAR (which also should be 1-based) and when you have all the reads modify the resulting output files.

Does this help?

Cheers, Tobias