DelphIONe

I have **~33 000 mapped short reads** (~200pb) from Nanopore **RNA direct** run and I try to train a model to rebasecall and improve the mapping (reduce the number of...

duplex and nanopolish still make sense after assembly ?

1

I wonder if the use of Nanopolish after a canu assembly processed on duplex reads is still of interest in your opinion? If yes, is it possible ? Thanks Jared...

Hi! I try to use the command tombo build_model estimate_reference but I obtain this error : tombo build_model estimate_reference --fast5-basedirs fast5_gzip_single/ --tombo-model-filename noQ --processes 4 --corrected-group RawGenomeCorrected_001 --basecall-subgroups BaseCalled_custom [15:36:46]...

none barcode

1

Hi, Normally, I have no problem with Porechop. But on my multiplex cDNA run (SQK-LWB001 same barcode than BC, I have checked on nanopore site), Porechop find 0 barcode, it...

none correlation between modification position and +/- 1

2

Hi Marcus, Your tool is the only one that allows you to do an analysis per read, it's very useful! Thanks for this. I have a sequence with a modification...

epinano_rms.py -> OverflowError: Python int too large to convert to C long

3

Hi, I tried using nanoRMS but got this result after a few hours : python3 ~/softs/nanoRMS/epinano_RMS/epinano_rms.py -R ../Schizosaccharomyces_pombe.ASM294v2.dna.fa -b spliceRNA.bam -s sam2tsv.jar Traceback (most recent call last): /softs/nanoRMS/epinano_RMS/epinano_rms.py", line 341,...

Dorado (by modkit dmr) gives different results between replicats

2

# 2 replicats sequenced with different version of MinKnow but the same dorado version used gives some extra 6mA not legitim Rep1 sequenced on May, Rep2 sequenced on November. Dorado...

how is calculate valid_coverage ? Different results between total read or subsample reads

3

I have mapped reads on my genome. I used modkit pileup and dmr pair using the IVT sample. If I sub-sample these reads and re-run modkit pileup and then dmr...