Results for "Bonobo and Neandertal genome sequencing"
Bio-Scripts
Pack a perl program with their dependencies on Ubuntu !
...hundreds of microbial genomes and highly contiguous reconstruction...SvABA: Structural variation and indel detection by local assembl...ecting structural variants in sequencing data using genome-wide local...n bacteria using whole-genome sequencing (WGS) data. It is particularl...1518 days ago
Install Ragout genome assembler
$ conda install -c bioconda ragout Collecting package metadata (repodata.json): done Solvi...4.4.0-py37_1 --> 4.3.0-py37_0 Proceed ([y]/n)? y Downloading and Extrac...1471 days ago
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 }'1400 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.gz1372 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.c...| sed 's/^chr//' | sed 's/Cp/Pt/' > tmp mv tmp xxx.chrom.sizes gunzip -c genome_fil...1372 days ago
- Use pen and paper the assemble it. If you are brave enough, you can try to assemb...AGCCGGACCT TATGATCATT TCATTAGGCG AGGCGGAGCT HINT: There is NO sequencing errors HINT: Overlaps are...
1222 days ago
Create random 10000 SNPs in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq SGDref.R64-...rsion/translocation simulation. This simulation use the random...titv_ratio = 0.5 [Sun Jan 10 16:05:57 2021] Introducing random SNPs...1217 days ago
Create random 1000 INDEL in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuSNP.simseq.genome.fa -indel_count 1000...ocation simulation. This simulation use the random seed: 1678440514 The option...0.5 [Sun Jan 10 16:14:00 2021] Introducing random INDE...1217 days ago
Create random 1000 CNVs in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuINDEL.simseq.genome.fa -cnv_count 100 -prefix simuC...ation. This simulation use the random seed...unt = 100 The option duplication_tandem_dispersed_ratio has been speci...ain_loss_ratio = 1 > duplication_tandem_disp...1217 days ago
Create random 5 inversions in genome !
(base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuCNV.simseq.genome.fa -inversion_count 5...ocation simulation. This simulation use the random seed: 639103429 The option...000 [Sun Jan 10 16:30:40 2021] Introducing random Inve...1217 days ago
