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