Valentín Ignacio
Valentín Ignacio
Hello I have paired end reads from metagenomic libraries, ahead to estimate distances between these read sets should I concatenate the fastq files and then apply dist command? this is...
Hello I have performed a search using as query nucleotide multifasta and as a target an aminoacidic multifasta. The alignment is performed at aminoacidic level by translating the nucleotide multifasta....
Hello I want to build my own database (GTDB + own built MAGs). I used prodigal to convert my nucleotide fasta files to protein fasta files. As I see prodigal...
Hello I was using mash before with a set of paired end reads, the issue is that now I'm using the `-r` flag as recommended when sketching reads (metagenomic reads),...
Hello , I just want to understand what happens to the iterative assembly on each k-mer step. Lets say I have a read set of different lengths. the minimum read...
Hello, I'm trying to run a next strain analysis using gisaid data. (export augur needed data from gisaid). After exporting the data (fasta and metadata files). I made my own...
Hello I previously ran cd-hit on a HPC to dereplicate some contigs with no problem `cd-hit-est -i 10k_seqs.fasta -o cdhit_outdir/contigs_cd-hit -c 0.95 -n 8,9 -G 0 -aS 0.8 -g 1...
Hello Im trying to install sepia using the rust package provided by conda This is what I have done: `conda create -n sepia -y && conda activate sepia` `git clone...
Hello, I'm trying to count the gene abundance from Metagenomic libraries using `htseq-count program` from blast otuput format table 6 I converted it into a gff file with `blast2gff`, after...
Hello I installed racon via conda `conda install racon` I made my SAM file using bwa. then I run racon: `racon -t 20 joined_reads.fastq UlvaAlignContIlu.sam ulvacomp.contigs.fasta > polished_contigs.fasta` I got...