2084 days ago
Samtools commands for bioinformatician !
...rence samtools tview sal_sej_sorted.bam.bam sal_ref_sej.fasta ### results into txt file samtools depth /path/to/sorted_bam.bam > /path/to/coverage_results.txt ### note: returns count...1612 days ago
Pack a perl program with their dependencies on Ubuntu !
...here. To know more visit here: https://www.lazoi.com/Home Comparative Genomics !!This group is dedicated to Comparative genomics ... Dramatic results have emerged from the rapidly...1520 days ago
1167 days ago
Corona variant calling steps !
...ile" .fasta) echo $basename mkdir -p results/sam results/bam results/bcf results/vcf...ls sort -o results/bam/$basename.sorted.bam results/bam/$basename.aligned.bam...t_Results" cp -r results/bcf/*.vcf Variant_Results/ rem mkdir "Variant_Result...1054 days ago
999 days ago
Rules to run fastp / Snakemake !
...NPUT + "/{sample}-read_2.fq" output: fwd=RESULTS + "/fastq_trimmed/{sample}.1.trimmed.fastq", rev=RESULTS + "/fastq_trimmed/{sample}.2....ple}.json" threads: 5 log: RESULTS + "/logs/fastp/{sample}.prepr...910 days ago
Run Pango on your multifasta file !
...ng: Trying to unpickle estimator DecisionTreeClassifier from version 0.24.2 when using version 1.0.1. This might lead to breaking code or invalid results. Use at your own risk. For mo...896 days ago
Perl script to parse blast results and plot basic stats !
#!/usr/bin/perl use strict; use warnings; use List::Util qw(sum); # Usage: ./parse_blast.pl blast_result.txt die "Usage: ./parse_blast.pl blast_result.txt\n"...103 days ago
Python script to finds extact similar sequence between two multi fasta files !
...r running BLAST:") print(stderr) def parse_blast_results(output_file): # Parse BLAST results with open(output_file, "...ubject_file, output_file) # Parse and print BLAST results #parse_blast_results(out...12 days ago