Jared Simpson
Jared Simpson
It is a set of .tsv files, called from the main pipeline script here: https://github.com/jts/methylation-analysis/blob/master/pipeline.make#L365
They are tab-separated files containing the measured event levels for a particular k-mer, as output by `methyltrain`. This script is not meant to be run standalone, it is part of...
Hi Kim, SGA represents read IDs using a 32-bit integer to save space. This limits the maximum data set size to just over 4 billion reads. It looks like your...
Good catch. I just noticed you'll need to change this one as well: https://github.com/kimrutherford/sga/blob/2572d3528e626c6d8f7ff487ada37eed9d1d8567/src/SuffixTools/SAReader.cpp#L79 It should really be refactored so that all these read from SSA_INT_TYPE. Jared On Thu, Oct...
Hi Kim, Can I close this issue?
Hi, The fast5 file structure has changed a lot since 2015 and R7 data is no longer well supported. If you want to exactly replicate the analysis for our paper...
Yes, all modern ONT data will contain /Raw/Signal. We've tried to maintain support for older data in nanopolish but since no one really uses R7 data anymore some features may...
Hi, This repository is largely unmaintained so I apologize for the poor documentation and lack of error handling. This error is likely because minimap2 is not found on your PATH....
Is `samtools` available on your PATH as well?
Both of those are python packages - can you try to install them using pip? Jared On Thu, Sep 10, 2020 at 1:20 PM Ashma Chakrawarti wrote: > Thank you,...