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GoekeLab
Identification of differential RNA modifications from nanopore direct RNA sequencing
Hi team, I want to compare m6a levels between my samples among other analyses. I first ran m6anet to get sample level m6a output and didn't have the foresight and...
Hello. I am having problems with the output file from the dataprep stage. This is the code I am running: ``` xpore dataprep \ --eventalign /ibex/tmp/c2078/Heat_stress_analysis/xpore/data/25rep1/eventalign.txt \ --out_dir /ibex/tmp/c2078/Heat_stress_analysis/xpore/data/25rep1/dataprep \...
Hi, I updated to the version 2.1 but still shows v2.0 when -v Best, Nick
Hello, I am using xpore to analyze example data, but I noticed that some of the motifs in the output do not contain any A or T. Given that xpore...
Hi, I got the following error when I ran `xpore diffmod` ``` Loading python/3.9.13 Loading requirement: gcc/7.2.0 readline/8.1 curl/7.74.0 libxml2/2.9.1 pcre/8.44.utf8 libpng/1.2.59 sqlite/3.35.3 geos/3.4.2 libtiff/4.0.9 proj/7.2.0 tcltk/8.6.11 CpG-tools/1.1.0 Using the...
Hi @yuukiiwa I wonder if there's a way to get m6A level, which can be defined by the number of m6a-modifying copies out of total number of copies of each...
hello i'm trying to analyze m6A modification of our direct RNA seq data with Xpore. does Xpore work with only one sample..?
i am doing nanopolish-eventalign for my nanopore direct RNA sequence reads. I have 9 samples, for a sample the command is running for more than 24 hours and is not...
Hello，after using `xpore dataprep --eventalign eventalign.txt --out_dir dataprep`， it output a datarep file, but it is only 8m in size. When I open data.log, it shows： Total 1 transcripts -...
My team recently ran xPore on both an RNA002 and RNA004 dataset. The RNA004 dataset, understandably, resulted in some pretty strange outcomes. In particular, the RNA004 output seemed to have...
