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dincarnato / RNAFramework

RNA structure probing and post-transcriptional modifications mapping high-throughput data analysis
http://www.rnaframework.com
GNU General Public License v3.0
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rc file to mm file #59

Open Asperatus22 opened 5 months ago

Asperatus22 commented 5 months ago

Hi Danny, I merged replicate to better cover some transcript with succes. I would try draco on this experiment but while rf-map generate a .mm file, rf-rctools merge does not. Is there a way to convert rc file to mm? One more time thanks for you work. Lionel

dincarnato commented 5 months ago

Hi Lionel,

Unfortunately you cannot go from RC to MM. The MM stores every single read, while the RC only stores transcript-level counts. In future releases I will add MM manipulation to rf-rctools, but for the moment my suggestion is to merge the BAM files and reprocess the merged file with rf-count to get a new MM file.

If that's too time consuming, let me know and I'll see if I can get you a simple script to merge two MM files.

Cheers, Danny

Asperatus22 commented 5 months ago

Hi Danny, As rf-count is one of the most time consuming job, i think a script to merge two MM files will be the best option. Thanks a lot Lionel

dincarnato commented 2 days ago

Hi Lionel,

the latest RNA Framework is not online. While merging of MM files is not possible yet, the new rf-count has multithread support (on a transcript basis, meaning that multiple transcripts are processed on separate threads) which should significantly speed up runtimes. Would you mind give it a shot and let me know? Also, the issue in rf-eval has been solved.

Cheers, Danny