Results for "Genome Size"
Bio-Scripts
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 }'1395 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.gz1367 days ago
Bash script to get intergenic region from genome files !
...ergenic region, we will require the size of the chromosomes. wget http://xxx.chrom.sizes cat xxx.chrom.sizes | sed '...'s/Cp/Pt/' > tmp mv tmp xxx.chrom.sizes gunzip -c genome_file.gtf.gz | awk 'BEGIN{O...ls complement -i stdin -g xxx.chrom.sizes | gzip > my_intergenic.bed....1367 days ago
- (JitMetaENV) ➜ assembly conda install -c bioconda prokka Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen s...
1217 days ago
- Use pen and paper the assemble it. If you are brave enough, you can try to assemble this set of reads: CAGATGTCCT GACCTTTTCT TAAGATCTTT TCTTTAGCCG TT...
1217 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 .....1213 days ago
Create random 1000 INDEL in genome !
...Study git:(master) ✗ perl ../simuG.pl -refseq simuSNP.simseq.genome.fa -indel_count 1000 -prefix...atio has been specified: ins_del_ratio = 1 The option indel_size_powerlaw_alpha has been specified: indel_size_powerlaw_alpha = 2 The optio...1213 days ago
Create random 1000 CNVs in genome !
...pStudy git:(master) ✗ perl ../simuG.pl -refseq simuINDEL.simseq.genome.fa -cnv_count 100 -prefix sim...as been specified: cnv_max_copy_number = 10 The option cnv_min_size has been specified: cnv_min_size = 100 The option cnv_min_siz...1213 days ago
Create random 5 inversions in genome !
...pStudy git:(master) ✗ perl ../simuG.pl -refseq simuCNV.simseq.genome.fa -inversion_count 5 -prefix...been specified: inversion_count = 5 The option inversion_min_size has been specified: inversion_min_size = 1000 The option inversion_...1213 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 Jan 10...1213 days ago
