sjfleck

I've installed a few different MaSuRCA versions, but I don't recall getting these errors in the past. This is for the new 4.1.0 version. I have a txt file attached...

CD-HIT not working (empty error file)

1

I have a very large multi-FASTA file containing many replicate nucleotide sequences. With smaller files, I've dealt with duplicates using BBedit, but this file is way too big to do...

Thank you for this interesting and useful program. I have a question about this step: samtools mpileup -C 50 -uf ref.fa aln.bam | bcftools view -c - | vcfutils.pl vcf2fq...

TreeShrink error

8

I ran 3 PASTA commands, only 2 of which were successful: 1. PASTA with default parameters (SUCCESS) _run_pasta.py -d PROTEIN -i protein_sequences.txt -o pasta_job_ 2. PASTA with RaxML (SUCCESS) _run_pasta.py...

'make all' warning & 'make test' error: invalid syntax

2

Hi all, I'm having an issue with 'make all' and make test. I'm using a lua system to load modules. **Commands:** git clone https://github.com/benedictpaten/sonLib.git cd sonLib module use -a /projects/academic/vaalbert/modulefiles/Allluas...

unexpectedly low depth of coverage after mapping with MiniMap2

3

Hello, I have 3 samples I'm working with. By comparing the total ONT sequenced read length and the estimated haploid genome sizes sample 1: 24.96x coverage sample 2: 22.36x coverage...

Output issues for the -w, -x, and -y options

2

My goal is to create a genome guided transcriptome assembly using Stringtie and use gffread to convert the output GFT into a GFF3. I seem to be able to create...

r10.4 e8.1 base calling

1

Can I use this version of Guppy to base call reads that have r10.4 flow cells and e8.1 enzyme? I believe the guppy base caller version was v5.0.15

looking at some very recent polyploidy events and species splits with ksrates

12

Hello, Thank you for making this tool. It have been useful for a few research projects already. Does ksrates remove paralogous ks anchor pair data smaller than 0.05? If so,...