Results for "quality check"
Bio-Scripts
Installing pb-assembly on Linux !
[jnarayan@hmem00 ~]$ module avail --------------------------------------------------...ure that releases on Bioconda live up to the # # quality that PacBio strives for, we m...ure that releases on Bioconda live up to the # # quali...2077 days ago
- (denovo_asm) [jnarayan@hmem00 ~]$ git clone https://github.com/cdunn2001/git-sym.git...-sym-local/links', '/home/users/j/n/jnarayan/FALCON-examples/.git-sym') git: 'check-ignore' is not a git command....
2077 days ago
Setting up falconUnzip conda environments for genome assembly !
➜ Analysis_Results conda create -n denovo_asm Solving environment: done ## Package...ure that releases on Bioconda live up to the # # quality that PacBio strives for, we m...ure that releases on Bioconda live up to the # # quali...2033 days ago
- # Convert FASTQ to FASTA seqtk seq -a IN.fastq > OUT.fasta # Convert FASTQ to FASTA and set bases of quality lower than 20 to N seqtk seq -aQ64 -q20 -n N IN.fastq > OUT.fasta # Download Seqtk https://github.com/lh3/seqtk
1768 days ago
Perl script to run in parellel !
#!/usr/bin/perl use strict; use warnings; use Parallel::ForkManager; use Bio::Se...rts fine if ($sequence_data{$accession_number}{status} eq "OK") { # Add check points here...1730 days ago
Samtools commands for bioinformatician !
## count mapped reads samtools view -c -F 260 mapping_file.bam ### converting sam file into fasta...pecified samtool view -c -f 4 sal_sej.bam ### count reads by quality value specified (-q) (>=) # -q : minimal quali...1646 days ago
Bash commandline to install Anaconda !
#The line begins with $ are the commands $ mkdir tmp $ cd tmp/ $ curl -O https://repo.anaconda.com/archive/Anaconda3-2019.03-Linux-x86_64.sh % Total %...1598 days ago
Bash command to install bwa, samtools, picard !
(base) [wsu29@bladeamd-2 tmp]$ conda install bwa Collecting package metadata (repodat....json): done Solving environment: - The environment is inconsistent, please check the package plan carefully T...1598 days ago
Perl script to delete the adjacent repeats !
/usr/bin/perl #Mostly the interview question for bioinfomatician ! #Write a code...rted to ATGC $string =~ s/(\w)\1/$1/g; print $string; #For more helps ... check out this #This bit of code...1594 days ago
- (py36) [wsu29@bladeamd-2 lofreq]$ lsb_release -a LSB Version: :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch Distributor ID: CentOS Description: CentOS release 6.7 (Final) Release: 6.7 Codename: Final
1581 days ago
