Results for "c"
Bio-Scripts
Bash script to get intergenic region from genome files !
#For the intergenic region, we will require the size of the chromosomes. wget http://xxx.chrom.sizes cat xxx.chrom.sizes | sed '...//' | sed 's/Cp/Pt/' > tmp mv tmp xxx.chrom.sizes gunzip -c genome...| bedtools complement -i stdin -g xxx.chrom.sizes | gzip > my_interg...1422 days ago
Bash script to handle Multifasta files
#Convert all lowercase residues to uppercase in a FASTA sequence file $ awk 'BEGIN{FS=" "}{if....fasta #Rearrange FASTA sequences according to their length...th($2),$0;)}' |\ >sort -k1,1n | cut -f 2- |tr "\t" "\n" > outpu...#Merge all FASTA files in a directory into a single FASTA file...1414 days ago
- #!/usr/bin/perl use strict; use warnings; #assign strings to variables my $DNA = "GATTACACAT"; my $polyA = "AAAA"; #concatenate two strings my $mo...ifiedDNA has length $DNAlength\n"; #extract the second codon in $modifie...
1397 days ago
Print the screenshot of read coverage remotely !
#Chrom_2:9700000-9760000 ASCIIGenome -ni --fasta A_vaga.NDPD.fasta -r Chrom_2:9700000-9760000 -x "save >> test.pdf" A_vaga.NDPD.fasta.out.sam.bam.sorted.bam1340 days ago
Install SibeliaZ in your Linux cluster !
...nv) jitendra@Bathymodiolus:~$ conda install -c bioconda sibeliaz Collecting package metadata (current_repodata.json): done S...he1b5a44_0 61 KB bioconda openssl-1.1.1i...ackages will be UPDATED: ca-certificates...1289 days ago
- JitMeta (base) ➜ JitMeta conda create --name JitMetaENV Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.
1274 days ago
- (JitMetaENV) ➜ JitMeta conda install grabseqs -c louiejtaylor -c bioconda -c conda-forge Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.
1274 days ago
- (JitMetaENV) ➜ JitMeta conda install -c bioconda fastqc Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.
1273 days ago
Install trimmomatic using conda !
(JitMetaENV) ➜ fastQC_out conda install -c bioconda trimmomatic Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.1273 days ago
- (JitMetaENV) ➜ fastQC_out trimmomatic SE -phred33 SRR5322499_1.fastq out.trimmed.fast...ILING:3 SLIDINGWINDOW:4:15 MINLEN:36 TrimmomaticSE: Started with arguments:...RAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 Automatically using 1 threads Input Re...
1273 days ago
