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GoekeLab / xpore

Identification of differential RNA modifications from nanopore direct RNA sequencing
https://xpore.readthedocs.io/
MIT License
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xpore MinION data access #59

Closed sumin5784 closed 2 years ago

sumin5784 commented 3 years ago

Hello :)

I've been looking for HEK293T cell line nanopore sequencing data, and thank you for the sharing the data.

I have some questions about SRA accession IDs.

There are WT-rep1,2,3 and WT0/25/50/75/100-1,2,3 replicates in accession list. What are the differences between WT and WT0/25/50/75/100? Also, could you inform me the differences between KO, KD, and KD-Ctrl samples?

I already downloaded HEK293T-WT-rep1,3 and HEK293T-KO-rep1,3. WT-rep1 and KO-rep1 are both seemed correct. But WT/KO-rep3 has 5~6 subfolders and each folder contains only several fast5 files. It seems like it has only a few reads, is there any specific reason for this?

Bests, Sumin

jonathangoeke commented 3 years ago

Hi @sumin5784, Can you post your question in the discussion forum? https://github.com/GoekeLab/xpore/discussions/new Others will then be able to read the answer as well. Any issue directly related to the xPore implementation feel free to post as an issue. Thanks! Jonathan

sumin5784 commented 3 years ago

Sure!