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pseudouridylation extracting #193
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Dear Ranj, (Not the developer) You can see how I've implemented Modkit for this question in this notebook: https://github.com/Theo-Nelson/SMS-colab/blob/main/C8/HCV_AND_METTL3_KO_ANALYSIS.ipynb Unfortunately, it seems like there are places which call both pseudo-Uridine and m6a simultaneously - this indicates to me at least that there is some kind of bug. I have not had a chance to track this further. Sincerely, |
Hello @Papareddy, It depends what you're trying to test with your experiment. If you want to find pseU positions, you could try using Do you mean that there are genomic positions with a bedmethyl record for pseU and m6A like this?
and
The explination for this is as follows, take the first example. The reference has a e.g. $ modkit pileup ${mod_bam} - | awk '$4=="17802"' > pileup_pseU.bed
# or
$ modkit pileup ${mod_bam} pileup_all_mods.bed
$ awk '$4==17802' pileup_all_mods.bed > pileup_pseU.bed Hope this helps, happy to answer any additional questions. |
Hello @Papareddy, Feel free to re-open this issue if you have any additional questions. |
Hi,
Thanks for this nice piece of software.
With Dorado 0.7, pseudouridination can be predicted. I was wondering if you have any tips and manual on how to identify PseU from the bam file generated after basecalling Modkit?
Cheers,
Ranj
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