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GoekeLab
Identification of differential RNA modifications from nanopore direct RNA sequencing
Hi there I would like to thank you for developing this beautiful program to analyze nanopore dRNA-seq data. I started from raw data processing before running the xpore, which I...
Hi all, I'm trying to run the demo code found here: https://xpore.readthedocs.io/en/latest/quickstart.html I'm able to create the dataprep folders correctly for both WT and KO datasets (I have the "---...
Hi, xpore diffmod can calculate " Pairwise comparison without replicates with default parameter setting." I'd like to maker sure that I can only have two input files. Is it possible...
Hello, thanks for your great tool! Recently I am trying to run xpore on my data, however, there is an error stating that: ` File "pandas/_libs/lib.pyx", line 2411, in pandas._libs.lib.maybe_convert_numeric...
Hi, I have three replicates of treated and WT for comparison. In the final result table, I see that in some sites, only one of the replicates has a mod...
## Summary xPore v2.1 has some minor changes from the previous version, which include the following. - Fixed a bug in `dataprep`, which can now handle transcriptome fasta files without...
Hi, I keep getting an error message and empty output files (data.index, data.json, data.log, data.readcount eventalign.index) when running the xpore dataprep step for genomic coordinates. I have downloaded the latest...
Dear xpore developers, I ran xpore on two SARS-CoV-2 samples to compare variant differences. After running xpore dataprep and then xpore diffmod I only receive information for about 2500 out...
Hi, I have concern about the dff table, How does the P value calculated? I have 2 time points in my experiment, one of them (9_hpi) only and has one...
Tombo can generate per-read statistics for differential modification. Based on the xpore approach described in your paper, xpore should also be able to compute mixture weights for each read. Does...
