Bash script to alignment of short reads against reference genome !
...E.coli_K12_MG1655.fa SRR1770413_1.fastq.gz SRR1770413_2.fastq.gz \ | samtools view -b - >...STQs E.coli_K12_MG1655.fa SRR1770413_1.fastq.gz SRR1770413_2.fastq.gz --- thi...E.coli_K12_MG1655.fa SRR341549_1.fastq.gz SRR341549_2.fastq.gz \...1562 days ago
Installing ggplot2 and its dependencies on Ubuntu !
...project.org/src/contrib/ellipsis_0.3.0.tar.gz' Content type 'application/x-gzip' length 7371 bytes =======....r-project.org/src/contrib/vctrs_0.2.2.tar.gz' Content type 'application/x...1.4.3.tar.gz' Content type 'application/x-gzip' length 230874 bytes (225 K...1552 days ago
Install Parrot Virtual Machine !
...ftp://ftp.parrot.org/pub/parrot/releases/supported/8.1.0/parrot-8.1.0.tar.gz jit@jit-HP-Pro-3335-MT:~/Downloads/parrot-8.1.0$ tar -zxvf parrot-8.1.0.tar.gz parrot-8.1.0/ jit@jit-HP-P...1540 days ago
1528 days ago
Correct bash command to zip your vcf file
bgzip -c file.vcf > file.vcf.gz tabix -p vcf file.vcf.gz #More at http://www.htslib.org/doc/tabix.html1526 days ago
1444 days ago
Sequence Ids conversion files !
...:00 special_requests/ 18/04/2020, 00:15:00 737 B 09/06/2011, 05:30:00 ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2accession.gz ftp://ftp.ncbi.nlm.nih.gov/g...1405 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.gz1368 days ago
Bash script to extract intronic fragments !
...e genic region, we have the intronic region. gunzip -c genome_file.gtf.gz | awk 'BEGIN{OFS="\t";} $3==...1,$4-1,$5}' | bedtools sort | bedtools subtract -a stdin -b my_exon.bed.gz | gzip > my_intron.bed.gz1368 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==...-g xxx.chrom.sizes | bedtools complement -i stdin -g xxx.chrom.sizes | gzip > my_intergenic.bed.gz...1368 days ago