Results for "NT"
Bio-Scripts
Install Install Gffcompare on Ubuntu / Linux
#Gffcompare is a program that is used to perform operations on general feature format (GFF) and general transfer format (GTF) files. It has a binary distribution comp...884 days ago
- #R is a feature rich interpretive programming language originally released...installing additional packages easier. We’ve commented out the code below, however...e code cd R-3.5.1 ./configure --prefix=/home/ubuntu/workspace/bin --with-x=no m...
884 days ago
Install StringTie on ubuntu / Linux !
#StringTie is a software program to perform transcript assembly and quantification of RNAseq data. The binary distributions are available so to install we can just download this dis...884 days ago
Install Varscan on Ubuntu / Linux !
#Varscan is a java program designed to call variants in sequencing data. It was developed at the Genome In...thub. To use Varscan we simply need to download the distributed jar file into our ~/workspace/bin. As with...884 days ago
Bash script to split multifasta file !
...sing awk, we can easily split a file (multi.fa) into chunks of size N (here, N=50...awk 'BEGIN {n=0;} /^>/ {if(n%500==0){file=sprintf("chunk%d.fa",n);} print >> f...(grep ">" multi.fasta -c) 'BEGIN{n=0; chunksize=int(chunksize/10)+1 } /^>/ {if(n%...884 days ago
BBmap the reads with all alignments !
bbmap.sh in=../reference/reference.numbered.fa ambig=all vslow perfectmode maxsites=100000 out=fetch_Ids_for_barcode.sam879 days ago
Commands to get the detail of disk usage on Linux !
#A simplistic approach would be du -shc /home/* du -shc /home/jnarayan #To sort it: du -smc /home/* | sort -n #There is also a wellknown Perl script that has the option of mailing disk usage reports per user: durep http://www.ubuntugeek.com/create-disk-usage-reports-with-durep.html876 days ago
Command line to print disk usage on Linux terminal !
#Print disk usage - perl du -h |perl -e'%h=map{/.\s/;99**(ord$&&7)-$`,$_}`du -h`;die@h{sort%h}' #Bash du -k * | sort -nr | cut -f2 | xargs -d '\n' du -sh #Base du -scBM | sort -n #More du -s * | sort -rn | cut -f2- | xargs -d "\n" du -sh875 days ago
- ...institute focused primarily on variant discovery and genotyping. It...conda which is a package, environment, and dependency management so...asically creates a virtual environment from which to run software. T...first start up the virtual environment with the command source activ...
872 days ago
Count number of lines in each file in Linux !
for FILE in *.rd; do wc -l $FILE; done > allReads.hits867 days ago
