get GC across the entire CDS !
#look at GC across the entire CDS. gffread -x - -g | \ seqtk comp - | \ awk -v OFS="\t" '{ print $1, "0", $2, ($4 + $5) / $2 }'1392 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.gz1364 days ago
Bash script to get intergenic region from genome files !
...the chromosomes. wget http://xxx.chrom.sizes 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...1364 days ago
1214 days ago
Create random 10000 SNPs in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq SGDref.R64-2-1.dups.fa -snp_count 10000 -prefix simuSNP [Sun Jan 10 16:05:57 2021] Starting simuG .. [...1210 days ago
Create random 1000 INDEL in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuSNP.simseq.genome.fa -indel_count 1000 -prefix simuINDEL [Sun Jan 10 16:14:00 2021] Starting simuG .. [Sun Jan 10...1210 days ago
Create random 1000 CNVs in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuINDEL.simseq.genome.fa -cnv_count 100 -prefix simuCNV [Sun Jan 10 16:24:20 2021] Starting simuG .. [Sun Jan 10 16...1210 days ago
Create random 5 inversions in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuCNV.simseq.genome.fa -inversion_count 5 -prefix simuINV [Sun Jan 10 16:30:40 2021] Starting simuG .. [Sun Jan 10...1210 days ago
Create random 2 translocations in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuINV.simseq.genome.fa -translocation_count 2 -prefix simuTRANS [Sun Jan 10 17:12:58 2021] Starting simuG .. [Sun J...1210 days ago
Commandline for paired end reads simulation with BBMap !
...0, max=0, unique=true insRate=0.0, max=0, len=(0-0) delRate=0.0, max=0, len=(0-0) subRate=0.0, max=0, len=(0-0) nRate =0.0, max=0, len=(0-0) genome=1 PERFECT_READ_RATIO=0.0 AD...989 days ago