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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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--only-mut issues #40

Closed catherine-douds closed 1 year ago

catherine-douds commented 1 year ago

Hi Danny,

I am having trouble getting the -om mutations to work as expected. I am only getting reactivities at G when I run the following code: rf-count -r -f file.fasta -m -la -ld -cc -mc 6 -q 30 -es -om G2T,G2C,A2N,T2N,C2N treated.bam untreated.bam

It seems like maybe it's only processing the first mutation? Do I have this formatted wrong?

dincarnato commented 1 year ago

Hi Catherine,

thanks a lot for reporting this! We made a change in the API and this slipped in between the cracks. It should be fixed now. Please issue a git pull. The issue was only occurring with IUPAC codes.

Let me know! All the best, Danny

catherine-douds commented 1 year ago

It worked! Thank you!

dincarnato commented 1 year ago

Great Catherine, I'll close the issue then!