xpore
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GoekeLab
Identification of differential RNA modifications from nanopore direct RNA sequencing
Hi, I am trying to install the last version (xpore 0.5.6 ) from pip but I got an error message: ``` pip install xpore==0.5.6 ERROR: Could not find a version...
I run following command and submitted to cluster using `qsub` on a `bigmem.q`: ``` #!/bin/bash # Set source of conda install source miniconda3/etc/profile.d/conda.sh conda activate xpore export baseDir=/analysisdata/rawseq/bcl/callum xpore-diffmod --config...
**I re-run nanopolish and start xpore-dataprep, but I got some errors in the log:** _2020-10-31 15:19:05,559 - pyensembl.shell - INFO - Running 'install' for EnsemblRelease(release=99, species='homo_sapiens') 2020-10-31 15:19:06,199 - pyensembl.sequence_data...
Hi @ploy-np , Can you give more details on how to understand the final results in *diffmod.table*?
I have been trying to run dataprep on some human data. I am using xpore version 0.5.4 installed using pip. The problem I am having is that all the files...
Hello, A option --n_processes is present in xpore-dataprep. Is that this option correspond to multi-threading ? Thanks in advance.
I am running xpore-diffmod with a reasonably large files and I get this error in the middle of the execution. Have you seen this error before? ``` [pm1122@gadi-hmem-clx-0013 WT2_RNAAB056712]$ /home/249/pm1122/raijin_home_2019-11-15/pm1122/lib/bin/xpore-diffmod...
I was wondering if xpore will work for (SQK-RNA001) dRNA sequence kit. Would it be any reasons to not work?
Hi @ploy-np thanks for the tool, it works really well! In the output: ``` id,position,kmer,diff_mod_rate_KO_vs_WT,pval_KO_vs_WT,z_score_KO_vs_WT,mod_rate_KO-rep1,mod_rate_WT-rep1,coverage_KO-rep1,coverage_WT-rep1,mu_unmod,mu_mod,sigma2_unmod,sigma2_mod,conf_mu_unmod,conf_mu_mod,m ENST00000273480.3,355,CTGTG,-0.08347772875845261,0.00045545433099164034,-3.505673042879497,0.9165081871312406,0.9999859158896932,135.00000000000003,71.0,99.48265403939226,104.17836035668046,28.4052619532913 ENST00000273480.3,593,CGATG,0.3427671649567362,7.343327455223234e-07,4.952056501330644,0.7507215520963253,0.4079543871395891,145.0,69.0,117.18091740473061,124.27790948192207,30.599099884885668,8.92729375396 ``` If i'm not wrong, every line gives information per site right? I...