Jumbled mess

Some linux commands that I keep forgetting and others !!

adding classpath in linux

export CLASSPATH = ${CLASSPATH}:/new/path

Adding perl path

export PERL5LIB=/path/to/your/installation/perl

Commands to print distinct column values

cut -d , -f2 file | sort | uniq

Export and set your path variable :-

export PATH=$PATH:/usr/local/bin

echo 'export PATH=$PATH:/usr/local/bin' >> ~/.bashrc

not match something in perl

@foo = grep(!/^#/, @bar);

BSUB job submission 

#BSUB -J TEST

#BSUB -o TEST.o%J

#BSUB -e TEST.e%J

#BSUB -q normal

#BSUB -n 1

#BSUB -R "rusage[mem=940]"

echo 'Hello world' > test.txt

one liner bsub :- 

bsub -R "rusage[mem=940000] span[hosts=1]" -J TEST -o TEST.o%J -e TEST.e%J -q normal -n 4 "echo 'Hello world' > test.txt"

Host static information : 

lshosts

Host dynamic info : lsload

Batch host info : bhosts

Job accept interval : bparams

bjobs example all jobs : bjobs -u all -a

bjobs example specific job : bjobs -l 303

Job history : bhist -u all 

Modifying job params : bmod -R "mem > 1000" 739

Further details can be found at : http://www.distributedbio.com/openlava/OpenlavaUserTraining.pdf

SCP how to

scp ~/rebels.txt dvader@deathstar.com:~/revenge

scp -r dvader@deathstar.com:~/revenge ~/revenge

scp dvader@deathstar.com:"revenge/*.txt" ~/revenge/

Alternative splicing packages in R

1. SplicingGraphs : http://www.bioconductor.org/packages/release/bioc/vignettes/SplicingGraphs/inst/doc/SplicingGraphs.pdf

2: 

Alternative splicing papers : 

http://genome.cshlp.org/content/23/5/789

Intron retention : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1370565/pdf/0100757.pdf

methylome map : http://openi.nlm.nih.gov/detailedresult.php?img=3280313_pone.0031621.g008&req=4

Regulation of alternative splicing by the core spliceosomal machinery : http://genesdev.cshlp.org/content/25/4/373.long

Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36 : http://www.nature.com/nsmb/journal/v18/n9/fig_tab/nsmb.2123_F5.html

Separate SNP from indels in a vcf file : awk script 

usage (awk -f file.awk file.vcf)

more details at : http://www.biostars.org/p/7403/

/^#/    {

    print $0 > "snv.vcf";

    print $0 > "indels.vcf";

    next;

    }

/^[^\t]+\t[0-9]+\t[^\t]*\t[atgcATGC]\t[a-zA-Z]\t/   {

    print $0 > "snv.vcf";

    next;

    }

    {

    print $0 > "indels.vcf";

    next;

    }

Locally installing R : 

http://onertipaday.blogspot.com/2008/04/r-installing-on-unixlinux-no-root.html

Interesting dictionary about everything bio : http://www.everythingbio.com