SquiggleKit

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Hi @Psy-Fer - as we discussed, a reminder to take a look at this when you have some time. :) It appears that it's difficult to build scrappie on MacOS,...

sirselim

Hello! I am new to nanopore signal processings and I was trying to run the MotifSeq in SquiggleKit. However each time I ran scrappie `scrappie squiggle my_kmer.fa > scrappie_kmer.model` I...

chilampoon

Fast5_fetcher_multi.py no output

2

Hello, I tried fast5_fetcher using follow cmd: `python3.6 fast5_fetcher_multi.py -p File.paf.gz -i /name.index --seq_sum sequencing_summary.txt.gz -o ./fast5_fetcher` but the only output i got is the error message: `no filenames list...

Salvobioinfo

SquiggleKit can be used for extract raw current signal in specific position of read?

3

Hi Thank you for you developing & maintaining this project :) I noticed that `squigglekit` can extract the current signal for a particular motif. So,I just wonder if it can...

weir12

Error plotting with SquigglePlot.py

8

Hi, unfortunately, I cannot get SquiggleKit to work. I closely followed your Installation tutorial and installed the required packages in a virtual environment. ``` cd /opt/bioinformatics git clone https://github.com/Psy-Fer/SquiggleKit.git python3...

capoony

Issue visualizing squiggles with recent fast5 file

3

Hi, I'm trying to visualize some squiggles from a recent fast5 file using SquigglePlot and the following command: ` python3 SquigglePlot.py -m -i /Users/marieke/data/test/FAO01221_pass_d7290dd7_3.fast5 ` However, when I try this...

mriekje

Job is in D state for a long time

10

Hi, I am trying to plot an individual fast5 file, and therefore installed the requirements to run: `python SquigglePlot.py -i ~/data/test.fast5` `(version python = 3.7)` However, after the script said...

kaltinel

Issue about MotifSeq.py.

1

Hi James, I ran the MotifSeq.py in the example dir of SquiggleKit like this: `python ../MotifSeq.py -p test.fast5 -m CATCTATCCAGGGTTAAATT.model > test_kmer.tsv` And it comes out with the error below:...

Goatofmountain

SquigglePull - KeyError: 'Unable to open object (component not found)'

2

> extract_fast5():failed to extract events or fastq from /Users/asttra/Documents/MATLAB/fMet_Bio_Reads/20190205_0545_MN16450_FAK54845_10d2f4d0/fast5/FAK54845_caf57096fcd614b49b6aa0a87f512b235585aff1_0.fast5main():data not extracted. Moving to next fileTime taken: 13.738579273223877 I'm getting this error for all of my files when using SquigglePull. I...

asttra

demultiplexing fast5

19

Hi From #14 It seems that MotifSeq could demultiplex a bundle of fast5 to retrieve the fast5 for each strains. Is this right? Or there is some options in Squiggle...

aspitaleri