Results for "PE"
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 compatible with the lin...883 days ago
- ...lls R to install without X11, a windowing system for displays. We’d also specify --prefix which is where t...ake and make install to build the software and copy the files to their proper location and create symlinks...
883 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...883 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 Institute at Washington University and is hosted on github. To use Varscan we...883 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.sam878 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.html875 days ago
Command line to print disk usage on Linux terminal !
#Print disk usage - perl du -h |perl -e'%h=map{/.\s/;99**(ord$&&7)-$`,$_}`du -h`;die@h{sort%h}' #Bash du -k * | sort -nr | cut -f2 | xargs -d '\n' du -sh #Base du -scBM | sort -n #More du -s * | sort -rn | cut -f2- | xargs -d "\n" du -sh874 days ago
- #GATK is a toolkit developed by the broad institute focused prim...ant discovery and genotyping. It is open source, hosted on github, an...ich is a package, environment, and dependency management software, in...reate, we also use the -p option to specify where this environment sh...
871 days ago
Multiline fasta to single line fasta !
perl -pe '$. > 1 and /^>/ ? print "\n" : chomp' in.fasta > out.fasta855 days ago
- #Commands to run PERF PERF --format fasta -t 30 -i reference.fasta -o PERF_output.tsv --include-atomic -m 2 -M 7 -l 12
851 days ago
