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GoekeLab
Identification of differential RNA modifications from nanopore direct RNA sequencing
Hello, I used the dataprep command for my in vivo sample with a depth around (~9000 reads) and it worked fine :+1: `xpore dataprep --eventalign /nanopolish/output.eventalign.txt --out_dir results --readcount_min 20...
Hi developer, I have successfully run my data with xpore. But I have a question, how could I distinguish which group has a higher m6A level in a single m6A...
Hi, can you please guide me on which reference file to use for direct human RNA? For nanopolish aligning, should the reference file be genome or transcriptome? Also, for xpore...
Hi, for the data preparation, I followed xpore docs. My data is direct RNA and used gencode transcriptome fasta file for the reference. And received 2T eventalign.txt files for each...
hi, I generated 2TB eventalign.txt using nanopolish as a result. Since it's nonsense storing it, I gzipped it and when I tried to apply xpore dataprep for the compressed eventalign.txt.gz,...
Hi there, I have a quick question about how to find the coordinate for the modification site. The output from xpore is the position relative to the start position of...
Hi Xpore team! I' d like to know if it is possible to run Xpore without a control sample (like KO sample), and this is the case where I only...
Hi - I'm having a problem running dataprep where the eventalign.index appears to run successfully but the data files do not eventalign.index output: > transcript_id,read_index,pos_start,pos_end > ENST00000457540.1|ENSG00000225630.1|OTTHUMG00000002336.1|OTTHUMT00000006718.1|MTND2P28-201|MTND2P28|1044|unprocessed_pseudogene|,15,172,97378 > ENST00000457540.1|ENSG00000225630.1|OTTHUMG00000002336.1|OTTHUMT00000006718.1|MTND2P28-201|MTND2P28|1044|unprocessed_pseudogene|,27,97378,302018 >...
Dear GoekeLab, I am trying to run xpore on the cluster of our institute, everythings goes well using the demo data, however I got this error/warning while running xpore dataprep...
Hello！ Thanks for such an excellent software, I have some doubts about diffmod.table. When I checked the Colum9 and Column10 of diffmod.table, I found that the minimum coverage is 15....
