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tleonardi / nanocompore

RNA modifications detection from Nanopore dRNA-Seq data
https://nanocompore.rna.rocks
GNU General Public License v3.0
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About SK1 transcriptome reference and m6A sites for Yeast #202

Open Derryxu opened 2 years ago

Derryxu commented 2 years ago

Hi, I hava two problem in learning nanocompore.

  1. The following files are provided in https://www.yeastgenome.org/strain/SK1 about reference file site mentioned in paper. Is the SK1_NCSL00000000_SGD_rna_genomic.fsa correct file for alignment ? Could you guide me on which Yeast SK1 transcriptome reference file to use for direct yeast RNA ? image

  2. In addition, Nanocompare compiled an orthogonal reference set of m6A sites from SK1 yeast by taking m6ASeq sites from Schwartz et al. andMAZTER-seq sites from Garcia-Camposet al. for benchmarking results against known yeast m6A sites. Is it possible to detail the processing of 1297 reference m6A positions？ I was unable to successfully reproduce as I can't find the sites file of MAZTER-seq clearly. Could the ground-truth m6a sites set file be shared please? Is there any way can obtain it?

Thanks very much! Best, xu

lmulroney commented 1 year ago

Dear Xu,

I'm really sorry that it has taken me this long to get back to you on this. I recently had to redo this analysis and couldn't exactly replicate the process used in the paper either, so I came up with a close approximation based on the description in the methods section of the nanocompore paper. You can follow the instructions on which references I used and on how to generate the m6A peaks file that I did in the github repository for NanOlympicsMod linked below.

https://github.com/mfurla/NanOlympicsMod/tree/main/Scripts

Look over these two files if you still need to replicate the work.

m6A_peaks_yeast_SK1_liftover.pdf convert_m6a_to_sk1.py

Again, sorry for the 1 year delay in getting back to you, and I hope that this information is still useful to your work after all this time.

All the best, Logan