gsukrit

Thank you for your response. Can you please suggest a possible way to map this position to the exact coordinate on the genome from the gff file, i.e. to 5'UTR/CDS/3'UTR...

Thank you for the information. That really gave some clarity. Can you suggest a possible approach / method to map these predicted positions to the exact gene coordinate and classify...

Hi team, So I tried running the suggested R2Dtool. The CHEUI output file (site_level_5mC_prediction) looked like this:  The command `bash cheui_to_bed.sh [cheui model II output file] [cheui_to_bed output file]`...

The command got executed without any errors this time. Thank you so much for the help.

Hi, I was able to execute the command without any errors this time. Thank you so much for the help. I have another query. The CHEUI documentation says these estimations...

Hi, Can you please let me know how to identify which of the fast5 is corrupted? I am using the fast5 directory of the reads classified under the "pass'' folder...

So When I ran the pileup command with --filter-percentile 0.1, letting modkit decide it;s own default

Hi, Thank you so much for responding. So I performed basecalling of both FAST5 (R9) and POD5 (R10 samples) using MinKnow software v24.11.10 (It bundles with dorado and calls it...

@ArtRand Hi, I was hoping to get some follow-up on what's the best way to proceed here.. Looking forward to your reply, Thank you!

Dear @ArtRand Thank you for taking a look. But isn't it weird that due to modkit's estimated threshold of 1, the final modification in A base is absolutely negligible in...