roblanf
roblanf
from: https://github.com/roblanf/sangeranalyseR/issues/32#issuecomment-597974547 @czliobio says: "Poly peak parser explain what the trace look like when the when a heterozygous indel exist. (https://doi.org/10.1002/dvdy.24183). However, it still needs reference sequence to determine the...
Just a note that we need to test on Mac, Linux, Windows Before we release. At least one user of the old version reported not being able to get it...
From this issue: https://github.com/roblanf/sangeranalyseR/issues/32#issuecomment-597974547 @czliubio says: "A standalone python script OverlapPER can merge reads into contig by overlap length and the minimum similarity, and then calculate the quality of consensus...
it should contain: 1. Primary base calls 2. Secondary base calls 3. Quality scores 4. Trimming information Other stuff?
potentially based on ab1 files from the folks at Westmead A few worked examples would be useful.
trimming removes bad bases from the ends, but what about bad bases in the middle? One option here is to remove reads based on other things, like the mean quality...
currently I output a table for each read which locates their secondary peaks w.r.t. the position in the read. What I need is an additional function that locates the secondary...
The idea here is that we want to trim aligned readsets according to some DNA reference sequence, before calling the consensus. It's not totally obvious whether it's better to trim...
One suggestion from Russ CD is to re-root on WH1, since i use that as a reference for the alignments. This would make mapping mutations more sensible looking.
This is recommended in the fastttree documentation: http://www.microbesonline.org/fasttree/#Gamma20 ``` If you want to use the traditional bootstrap instead, you can use phylip's SEQBOOT to generate resampled alignments, the -n option...