Bash script to alignment of short reads against reference genome !
...ew -b - >SRR1770413.raw.bam sambamba sort SRR1770413.raw.bam sambamba markdup SRR1770413.raw.sorted.bam SRR1770413.bam ##B...ndicates this) and converts to BAM. #sorting the BAM file: sambamba sor...>SRR341549.raw.minimap2.bam sambamba sort SRR341549.raw.minimap2.bam s...1574 days ago
1529 days ago
Command to sort the bed file !
#Command to sort the bed file sort -V -k1,1 -k2,2 test.bed1404 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.gz1381 days ago
Bash script to extract intronic fragments !
...the genic region, we have the intronic region. gunzip -c genome_file.gtf.gz | awk 'BEGIN{OFS="\t";} $3=="gene" {print $1,$4-1,$5}' | bedtools sort | bedtools subtract -a stdin...1381 days ago
Bash script to get intergenic region from genome files !
...| 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.sizes | bedtool...1381 days ago
Bash script to handle Multifasta files
...%s\t",(N>0?"\n":""), $0);N++;next;} {printf("%s",$0);} END {printf("\n");}' input.fasta |\ >awk -F '\t' '{printf("%d\t%s\n",length($2),$0;)}' |\ >sort -k1,1n | cut -f 2- |tr "\t" "...1372 days ago
1230 days ago
Corona variant calling steps !
...lts/sam/$basename.aligned.sam samtools view -S -b results/sam/$basename.aligned.sam > results/bam/$basename.aligned.bam samtools sort -o results/bam/$basename.sorted.bam results/bam/$basename.a...1060 days ago
1011 days ago