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Formatting Database for Blast+ =========================== To use any sequence by Blast/Blast+ , we need to format the fasta . Let's do it  for uniprot: 1. download uniprot from the link provided ============================= ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz 2. issue the following command for blast+: ============================= /home/apps/ncbi/blast+/2.2.29/bin/makeblastdb -dbtype prot -in /path/to/uniprot.fasta To get blast+ commands, if you are familiar with legacy blast, use legacy_blast.pl in the following way: $ /home/apps/ncbi/blast+/2.2.29/bin/legacy_blast.pl formatdb -i test.fasta -p T --path /home/apps/ncbi/blast+/2.2.29/bin --print_only /home/apps/ncbi/blast+/2.2.29/bin/makeblastdb -dbtype prot -in test.fasta

http://www.ece.uci.edu/~chou/ssh-key.html Setting up SSH public/private keys SSH (Secure Shell) can be set up with public/private key pairs so that you don't have to type the password each time. Because SSH is the transport for other services such as SCP (secure copy), SFTP (secure file transfer), and other services (CVS, etc), this can be very convenient and save you a lot of typing. SSH Version 2 On the local machine, type the BOLD part. The non-bold part is what you might see as output or prompt. Step 1: % ssh-keygen -t dsa Generating public/private dsa key pair. Enter file in which to save the key (~/.ssh/id_dsa): (just type return) Enter passphrase (empty for no passphrase): ...

http://stackoverflow.com/questions/3587025/jfree-charts-sample-tutorial http://www.screaming-penguin.com/node/4005 http://www.vogella.de/articles/JFreeChart/article.html http://adityanivas3.blogspot.com/2008/09/jfree-chart-tutorial.html http://www.javaworld.com/javaworld/jw-12-2002/jw-1227-opensourceprofile.html There's even some examples right in the code, such as the one described here: http://www.jfree.org/jfreechart/api/javadoc/org/jfree/chart/demo/TimeSeriesChartDemo1.html  // HOW TO CREATE CHART AND SAVE AS PNG         final XYDataset dataset = createDataset();         final JFreeChart chart = createChart(dataset);                 try {             File f1 = new File("myline.png");             ChartUtilities.saveChartAsPNG(...

Open Control panel sudo  /opt/lampp/share/xampp- control-panel/xampp-control- panel How to start / stop apache server in xampp sudo /opt/lampp/lampp start sudo /opt/lampp/lampp stop How to change default apache port 80 to another port: Find the line "Listen 80" in any of these files and change to new port number. /opt/lampp/etc/httpd.conf /opt/lampp/etc/original/httpd. conf

1. Download you iso file. say myfile.iso 2. Make a directory where it will be mounted sudo mkdir /mnt/iso 3. Mount the iso file there sudo mount -t iso9660 -o loop /home/Download/myfile.iso /mnt/iso/     4. Install it   ./myfile.iso

#!/bin/sh ##### PARAMTER for INTERSECT######: ## mention strandness # -s # print A , with number of Hit #  -c # print A , with number of bp overlap # -wo ##### EXAMPLE #### f1="coding.withrpt.bed.tmp" f2="noncoding.withrpt.bed.tmp" f1Out="coding.withrpt.bed" f2Out="noncoding.withrpt.bed" fCDS="refseqcoding.CDS.bed" # bedtools intersect -s -c  -a $f1 -b $fCDS  > $f1Out # bedtools intersect -s -wo  -a $f1 -b $fCDS  > $f1Out.bp # bedtools intersect -s -c  -a $f2 -b $fCDS  > $f2Out # bedtools intersect -s -wo  -a $f2 -b $fCDS  > $f2Out.bp # bedtools intersect -s -wo -a test1.bed -b test2.bed ##### PARAMTER for GETFASTA ######: ## mention strandness # -s ## input and output file # -fi  -fo ##### EXAMPLE #### fAllgeneBed="allGene.bed" fAllgeneFasta="allGene.fasta" # bedtools getfasta  -s  -fi /home/data/genomes/hg19/hg19.fa -bed $fAllgeneBed -fo $fAllgeneFasta

Some basic terminology used in RNA-seq papers http://thegenomefactory.blogspot.com/2013/08/paired-end-read-confusion-library.html Basic idea to calculate RPKM ( R eads P er K ilo exon per M illion mappedread) http://seqanswers.com/forums/showthread.php?t=2954 9 First of all, Cufflinks uses FPKM (Fragments Per Kilobase of exon per Million mapped fragments) instead of RPKM (Reads Per Kilobase of exon per Million mapped reads) to avoid confusion when dealing with paired-end data. Secondly, Cufflinks uses corrections when calculating FPKM, so if you do a simple calculation it will not match that of Cufflink's. Anyway, the crude calculation for a gene would be (NOT the one that Cufflinks uses): FPKM = [f / (e / 1000)] / (m / 1,000,000) f - number of fragments mapping to gene e - exonic length of gene m - total number of mapped fragments If you would like to know more about the corrections that Cufflinks applies to FPKM, see this paper: Trapnell C, Willi...