poreplex
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hyeshik
A versatile sequenced read processor for nanopore direct RNA sequencing
Hi @hyeshik First of all thank you for a great tool. It seems that it hasn't been updated in a while, so maybe it would be possible to add support...
Hi, I just tried demultiplexing a run with the following command: `poreplex -i fast5_pass -o demultiplexed --trim-adapter --barcoding --fast5` Which failed due to an unknown error according to the output:...
I have version 0.5 of poreplex installed both on a work server (linux) and on my own Mac. I am unable to get either of them working. If I run...
hello, Do you have instruction for training new set of barcodes? Thanks Amit
Hello, I got the following error: Unhandled exception KeyError: "Unable to open object (object 'Analyses' doesn't exist)" 2020-10-06 16:07:12,361 Starting poreplex version 0.4.1 2020-10-06 16:07:12,361 Command line: /apps/RH7U2/gnu/python/3.5.2/bin/poreplex -i /home/labs/schwartzlab/amitblum/nanopre_rawdata/L821_4_BCs1_4/L821_BC1_4/BCs1_4/20200923_1453_MN34379_FAO02325_d4e35397/fast5/...
2020-06-22 20:41:02,717 == Analysis settings ====================================== 2020-06-22 20:41:02,717 * Input: /mnt/raid62/BetaCoV/RawData/20200620/20200620_0916_MN27328_FAM92901_ea10d670/fast5_pass/ 2020-06-22 20:41:02,717 * Output: /mnt/raid62/BetaCoV/Person/tangchao/analysis/DrictRNA/Poreplex/output 2020-06-22 20:41:02,717 * Processes: 2 2020-06-22 20:41:02,717 * Presets: rna-r941.cfg 2020-06-22 20:41:02,717 * Basecall...
Hi, I tried to run poreplex on a minION run using the follwing command to basecall and demultiplex barcodes from direct RNA sequencing: ` poreplex -i 20191122_1000_MN24929_FAL01495_e9928ec8/fast5/ -o poreplex_demultiplex --barcoding...
Hi, I've installed poreplex 0.5 using: `git clone https://github.com/hyeshik/poreplex.git` `cd poreplex` `python3 setup.py install` I am using Ubuntu 20.04 terminal on Windows, python3.8.2 Trying to run the command: `poreplex --polya...
`==> Processing FAST5 files ERROR: Unhandled exception KeyError: 'read_id'Task exception was never retrieved` I coudln't find **read_id** nor **ERROR:** in the repository. How should I proceed? Or is it a...
Hello, It seems that numpy is needed for setting up installation with pip, otherwise the pip installer complains with: ``` Cache entry deserialization failed, entry ignored Using cached https://files.pythonhosted.org/packages/ce/41/99b51880c9d9835218978008cf75851f2257f9fe0271e5d76c96b17fe501/poreplex-0.4.tar.gz Complete...