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.gz1426 days ago
Bash script to extract intronic fragments !
#To obtain introns, we simply need the gene and exonic coordinates; #by subtracting the exonic regions from the genic region, we have the i...p -c genome_file.gtf.gz | awk 'BEGIN{OFS="\t";} $3=="gene" {print $1,$4-1,$5}' | bedtools s...1426 days ago
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 's...| sed 's/Cp/Pt/' > tmp mv tmp xxx.chrom.sizes gunzip -c genome_f...n -g xxx.chrom.sizes | gzip > my_intergenic.bed.gz1426 days ago
Bash script to handle Multifasta files
#Convert all lowercase residues to uppercase in a FASTA sequence file...t.fasta > output.fasta #Rearrange FASTA sequences accordin...put.fasta |\ >awk -F '\t' '{printf("%d\t%s\n",length($2),$0;...put1.fasta input2.fasta #Merge all FASTA files in a direct...1418 days ago
1401 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.bam1344 days ago
Install SibeliaZ in your Linux cluster !
...ollecting package metadata (current_repodata.json): done Solving environment: failed with initial fr...: failed with repodata from current_repodata.json, will retry...es will be UPDATED: ca-certificates...#################### | 100% Preparing transaction: done Ver...1293 days ago
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