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GoekeLab
Identification of differential RNA modifications from nanopore direct RNA sequencing
1、Can xpore detect 2'-O-Me ? If can, Has it been tested experimentally ？Do I need to adjust the xpore parameters？ 2、Can xpore detect two or three consecutive modification sites? If...
Hi, i am wondering how good is xpore detect other RNA modification like ψ and ADP-ribosylation or is it mainly designed for m6A/RNA methylation? Thanks in advance! Yun
running into problem with Xpore after merging multiple .fastq and .bam files from same Nanopore run
Dear Xpore developers, Thank you for the software. It was easy to install and handle , until I decided to merge all 50+ .fastq (and .bam) output files from one...
Dear @ploy-np and @yuukiiwa, @jonathangoeke, I downloaded preprocessed data of HEK293T-WT/KO-rep1,2,3 from https://doi.org/10.5281/zenodo.4587661 and run xpore 2.1 with those files. However, I didn't get any sites in the output file,...
Hi @yuukiiwa. Thank you for your tool, it's very nice. I have finished running my programs on human tissues, but I have a question. Could xpore be used in analysing...
Dear xPore team, I have run xpore on HEK293T-WT-rep1 and HEK293T-Mettl3-KO-rep1. I wish to compare my output diffmod.table and majority_direction_kmer_diffmod.table files with yours. Could you share the raw xpore results...
Hi, I have a question about Fig.2f in the xPore's paper. You mention about top significant 1,452 positions and use for compare with m6ACE-seq. So I download the Supplement1 and...
Dear xPore team, I've downloaded all the processed files of xpore paper's from Zenodo website, https://zenodo.org/record/5707193#.Y3rL9n1Bw2w. I found a file "Homo_sapiens.GRCh38.cdna.ncrna_wtChrIs_modified.fa". Does this file was modified to include cDNA, and...
Hello, I used the dataprep command for my in vivo sample with a depth around (1400X, ~9000 reads) and it worked fine +1 xpore dataprep --eventalign /nanopolish/output.eventalign.txt --out_dir results --readcount_min...
Hi, thank you for developing such an excellent tool! I encountered an error while running the `dataprep` function in the xpore software as follows: ```py KeyError Traceback (most recent call...
