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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...

1. First you have to have an account at noor. If not call ithelpdesk for that. 2. Then login as ssh -X  yourid@noor-login3.kaust.edu. sa 3. Load matlab under your account load matlab/R2012b 4.  Run matlab by following command /opt/share/MATLAB/matlab. R2012b Load matlab GUI =========== ssh -X  yourid@noor-login3.kaust.edu. sa module load matlab bsub -XF -I -q rh6_interactive matlab -desktop Following is the basic for using cluster noor: http://rcweb.kaust.edu.sa/ KAUST/ResearchComputing/wiki/ NoorGuid e Following is the basic for using any tool in noor cluster: http://rcweb.kaust.edu.sa/ KAUST/ResearchComputing/wiki/ up2speed

To get the number of processor ==================== less /proc/cpuinfo | grep processor To get the details of each processor and number of core ======================= # very detailed information less /proc/cpuinfo | less # summary information how many core/processor etc lscpu To get the RAM size ============= 1. In human readable format free -g free -m 2. In more details less /proc/meminfo  To get the disk size ============= 1. In human readable format df -h Total size of a folder =============== Enter into folder and then du -ch | grep total

Intro Gencode V3 GTF format is different from UCSC GFF/GTF. Here is the description of format. Gencode V3 GTF has 9 mandatory key=value pairs, which are not mandatory for UCSC GFF/GTF. Here is the description http://www.sanger.ac.uk/resources/databases/encode/gencodeformat.html Here is a code to convert bed file to Gencode v3 GTF format: import java.util.Vector; import java.util.regex.Pattern; import com.cbrc.bean.TrxExonInfo; import com.cbrc.common.CommonFunction; public class BedTools_BedToGencodeGTFv3 {         void convert_Bed_GencodeGtfv3( String fnmBed, String fnmGtf)         {                 String tmp[];                 Pattern p = Pattern.compile("[\\t]+");                 Vector vectBedStr = CommonFunction. readlinesOfAfile(fnmBed);                 Str...

y=[1:10]; mycell = cell(10,1); for i=1:5     mycell(i)=cellstr('mRNA prom'); end for i=6:10     mycell(i)=cellstr('lncRNA prom'); end    boxplot(y , mycell ,'notch','on','whisker',1);