Results for "LR"
Bio-Scripts
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,$5}' | bedtools sort | bedtools merge -i - | gzip > my_exon.bed.gz1365 days ago
- ...mparativeGenomics/wgd Requirement already satisfied: numpy>=1.16 in...om wgd==1.2) (1.19.0) Requirement already satisfied: scipy>=1.2 in...████| 32.4 MB 60 kB/s Requirement already satisfied: six>=1.5.2 in...██| 10.1 MB 38.9 MB/s Requirement already satisfied: pytz>=2011k in...
1207 days ago
Set up WGD environment using conda !
#Wgd cannot be installed directly with bioconda at present, so it is slightly troublesome to install, because it #depends on a lot of software. wgd depends on the fol...1202 days ago
- ...sembler *** The command line was: /home/urbe/anaconda3/envs/JitMetaENV/bin/bwise [Warning] /home/urbe/JitSimuStudy/test_phase_assebly directory already exists, BWISE will use it...
989 days ago
Commandline for paired end reads simulation with BBMap !
...genScaffoldInfo=true Writing chunk 1 Waiting for writing to finish. Finished. snpRate=0.0, max=0, unique=true insRate=0.0, max=0, len=(0-0) delRate=0.0, max=0, len=(0-0) sub...989 days ago
- ...tq k=`grep "^best k:" \ kmergenie-illumina-raw-reads.log | grep -Po "\d+"` echo "best k=${k}" # make 30x haploid coverage for PacBio CLR reads # error rate from 13 -...
927 days ago
Bash script to simulate a genome !
...upper.diploid.fasta.gz \ ziplevel=6 \ ploidy=2 \ subrate=0.0192 \ indelrate=0.001 \ maxindel=20 \ no...+"` echo "best k=${k}" # make 30x haploid coverage for PacBio CLR reads # error rate from 13 -...917 days ago
Run Pango on your multifasta file !
...bined.fa (pangolin) [jnarayan@hn1 FASTA]$ pangolin --update pangolin already latest release (v3.1.16)...olearn updated to 2021-11-18 constellations updated to v0.0.24 scorpio already latest release (v0.3.14)...886 days ago
- ...will be downloaded: package | build ---------------------------|----------------- backports.functools_lru_cache-1.6.4| pyhd3eb1b0_...
861 days ago
Installing SEVA environment in Conda !
...########################################################## | 100% r-modelr-0.1.8 | 218 KB | ###...########################################################### | 100% r-callr-3.7.0 | 440 KB | ##...837 days ago
