Rita Mormando

No log file and unclear data

5

I am using PacBio Hifi yeast genomes for this assembly and I would like to understand what the data is telling me: if the sequencing job was bad, if my...

kitsune and jellyfish error "Bloom filter file is truncated"

1

Hi I am trying to use the kitsune tool which uses jellyfish to calculate the best/optimal kmer size for counting but when I go to run the command I get...

Hello! For some reason everytime I run RagTag with the following command it adds "_RagTag" to the resulting headers of the FASTA file and I would like to get rid...

Hi I have a silly question when I go to run my command: `./pafCoordsDotPlotly.R -i /Volumes/MyPassport/mapping_s288c/alignments/sample.paf -o /Volumes/MyPassport/mapping/alignments/ -s -t -m 500 -l` It gives this error message: ``` 1:...

build step failed after throwing an instance of 'std::bad_alloc'

1

I am trying to build a kmer db using the k-mer output from KMC but I keep getting an error. This is the command I am running: ``` ./kmer-db build...

short read data

1

I have Illumina short-read sequences I want to use as an input will the tool take that into account when creating a database? The samples are labeled as`Sample1_R1.fasta Sample1_R2.fasta` would...

Duration and Heterozygosity

28

Hi I'm trying to run nPhase on a tetraploid yeast genome I seqeunced with PacBio HiFi reads. Here is my code: `nphase pipeline --sampleName trialRun1 --reference s288c.fa --longReads pacbioHiFireads.fastq.gz --longReadPlatform...

different assembler/fasta not working

2

Hello, I'm trying to use this tool to visualize differences in variants in yeast strains - specifically Saccharomyces cerevisiae S288C. I tried this code: ``` library(plotVCF) VCF please specify either...