Script to extract the cluster detail !
$ lsb_release -a No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 18.04.1 LTS Release: 18.04 Codename: bionic $ cat /proc/cpuinfo | grep -i 'model name' | head -n 1 model name : Intel(R) Xeon(R) CPU E5-2620 v4 @ 2.10GHz1434 days ago
Bash script to get exon fragments from genome files !
#Exons are already defined in the GTF file, so we simply need to print lines that are marked exonic. gunzip -c genome_file.gtf.gz | awk 'BEGIN{OFS="\t";} $3=="exon" {print $1,$4-1,$5}' | bedtools sort | bedtools merge -i - | gzip > my_exon.bed.gz1421 days ago
Bash script to extract intronic fragments !
#To obtain introns, we simply need the gene and exonic coordinates; #by subtracting the exonic regio...gunzip -c genome_file.gtf.gz | awk 'BEGIN{OFS="\t";} $3=="gene" {pr...4-1,$5}' | bedtools sort | bedtools subtract -a stdin -b my_exon.bed....1421 days ago
Bash script to get intergenic region from genome files !
...cat xxx.chrom.sizes | sed 's/^chr//' | sed 's/Cp/Pt/' > tmp mv tmp xxx.chrom.sizes gunzip -c genome_file.gtf.gz | awk 'BEGIN{OFS="\t";} $3=="gene" {print $1,$4-1,$5}' | bedtools sort -g xxx.chrom.size...1421 days ago
Bash script to handle Multifasta files
...rt all lowercase residues to uppercase in a FASTA sequence file $ awk 'BEGIN{FS=" "}{if(!/>/){print to...>sort -k1,1n | cut -f 2- |tr "\t" "\n" > output.fasta #Add ‘>’ at the beginning of headers in a FASTA...1413 days ago
1396 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.bam1339 days ago
Install SibeliaZ in your Linux cluster !
(jitenv) jitendra@Bathymodiolus:~$ conda install -c bioconda sibeliaz Collecting p...ded / updated specs: - sibeliaz The following packa...-py27_0 maf2synteny bioconda/linux-64::maf2synteny-...0% _anaconda_depends-20 | 6 KB | ######################...1288 days ago
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1273 days ago