Results for "B"
Bio-Scripts
...ased in 1995. It is heavily used in the bioinformatics community largely due to numerous R libraries available on bioconduct...ll go, this includes the additional R libraries we’ll download later. F...es easier. We’ve commented out the code below, however it is exactly wh...886 days ago
Install StringTie on ubuntu / Linux !
...ftware program to perform transcript assembly and quantification of RNAseq data. The binary distributions are availa...o install we can just download this distribution and extract it. Like wit...r.gz # make symlink ln -s ~/workspace/bin/stringtie-1.3.0.Linux_x86_6...886 days ago
Install Varscan on Ubuntu / Linux !
...me Institute at Washington University and is hosted on github. To use Varscan we simply need to download the distributed jar file into our ~/works...Varscan via java -jar. # Install Varscan cd ~/workspace/bin curl -L -k -o VarScan.v2.4...886 days ago
Bash script to split multifasta file !
...ly split a file (multi.fa) into chunks of size N (here, N=500), by using the following one-liner: awk 'BEGIN {n=0;} /^>/ {if(n%500==0)...multi.fa #OR awk -v chunksize=$(grep ">" multi.fasta -c) 'BEGIN{n=0; chunksize=int(chunks...885 days ago
BBmap the reads with all alignments !
bbmap.sh in=../reference/reference.numbered.fa ambig=all vslow perfectmode maxsites=100000 out=fetch_Ids_for_barcode.sam880 days ago
Commands to get the detail of disk usage on Linux !
#A simplistic approach would be du -shc /home/* du -shc /home/jnarayan #To sort it: du -smc /home/* | sort -n #There is also a wellknown Perl script that has the option of mailing disk usage reports per user: durep http://www.ubuntugeek.com/create-disk-usage-reports-with-durep.html878 days ago
Command line to print disk usage on Linux terminal !
#Print disk usage - perl du -h |perl -e'%h=map{/.\s/;99**(ord$&&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 -sh877 days ago
- #GATK is a toolkit developed by the broad institute focused primari...load and unzip GATK from github. The creators of GATK recomme...virtual environment for GATK by using the yaml file included..., we can then run the program by providing the path to the ex...
874 days ago
Count number of lines in each file in Linux !
for FILE in *.rd; do wc -l $FILE; done > allReads.hits869 days ago
Bash script to transfer files to server !
# rsync options source destination rsync -azvh --progress PacBio_clean.fa xxx@xxx.xxx.res.in:/home/ # scp source_file_name username@destination_host:destination_folder scp –rpv /datafile xxx@192.168.1.100:/home/me866 days ago
