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GoekeLab
Identification of differential RNA modifications from nanopore direct RNA sequencing
Hi @ploy-np, it would make xPore more widely useable if users were able to supply a valid GTF file to perform transcript to genome mapping instead of using pyensembl. It...
I have read the protocol in webpage of xpore (https://xpore.readthedocs.io/en/latest/preparation.html). It recomands us to mapping the long mRNA reads with the following commands "minimap2 -ax **map-ont** -uf -t 3 --secondary=no...
I ran into some error when running xpore-dataprep Command: `xpore-dataprep --eventalign wt1.fastq.evn.aln.tsv --summary wt1.fastq.evn.aln.summary.txt --out_dir wt1_xpore_data_prep` Error: Process Consumer-1: Traceback (most recent call last): File "/nfs/no_backup_isis/enovoa/analysis/hliu/software/XPORE/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 2646, in get_loc...
Hi developer, I'm trying to using the practice demo data downloaded from https://zenodo.org/record/5103099/files/demo.tar.gz, and I have successfully installed the latest version of xpore version 2.0. When I came to the...
Hi! Cool tool! thanks! I was wondering how xpore/xpore/diffmod/model_kmer.csv was calculated. Thanks a lot!
I downloaded and am using the latest xpore 2.0 release off github. 1. Basecalled all 3 replicates of each of the WT and KO Yeast SK1 from the epinano paper....
Per issue #73, an issue for a feature request to report on the methylation status and location for individual nanopore reads.
Per issue #73, a new issue to request support of GFF files as GTF files are older and GFF3 has been a standard for awhule.
Hi, When I download the datasets from PRJEB40872 in NCBI, however, I found a lot of data missing, such as HEK293T-Mett3-KO-rep2, HEK293T-WT-rep2, HEK293T-WT-100-rep1, HEK293T-WT-50-rep1, HEK293T-WT-50-rep2, HEK293T-WT-50-rep3, HEK293T-WT-25-rep2 and so on....
Hello, Thanks for providing this tool! I was wondering if the version of Guppy can have an impact on the prediction quality and performance. I have data called using Guppy...
