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RNA seq normalize read count RPKM= number of…
soirée rencontre celibataire à les chartreux RNA-seq; normalize read count RPKM=(number of mapping reads)*1000bp*1 million reads/[(length of transcript)*(number of total reads )] http://www.clcbio.com/manual/genomics/Definition_RPKM.html http://seqanswers.com/forums/showthread.php?t=10657 http://genomics.isi.edu/rnaseq/framework http://www.nature.com/nmeth/journal/v5/n7/pdf/nmeth.1226.pdf
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Sort files according to the creation time on…
Udalguri Sort files according to the creation time on Unix Sort by the last saved time ls -ltr Sort by the created time ls -lUr
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Save a Perl oneliner to a script perl…
Save a Perl oneliner to a script. perl -MO=Deparse -pe ‘s/(\d+)/localtime($1)/e’ http://stackoverflow.com/questions/2822525/how-can-i-convert-perl-one-liners-into-complete-scripts
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matchPWM is now part of Biostrings 2.7.47 in…
matchPWM() is now part of Biostrings 2.7.47 (in BioC devel, so you need R-2.7). Load Biostrings: library(Biostrings) Suppose ‘pwm’ contains a Position Weight Matrix, let’s say: pwm maxWeights(pwm) # the max weight in each column [1] 17 20 19 20 18 18 20 8 > maxScore(pwm) # the max possible score [1] 140 Let’s match…
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Installing Python without root http stackoverflow com questions…
Installing Python without root. http://stackoverflow.com/questions/622744/unable-to-install-python-without-sudo-access
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Quick and easy submission of R on Sun…
Quick and easy submission of R on Sun Grid Engine Easiest way to submit R jobs Here are two scripts and a symlink I created to make it easy as possible to submit R jobs to your Grid: qsub-R If you normally do something along the lines of: user@exec:~$ nohup nice R CMD BATCH toodles.R…
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When Mendeley bibliography duplicates instead of refreshing Check…
When Mendeley bibliography duplicates instead of refreshing. Check whether the following option is set in Word 2007: Office button->Word Options->Advanced->General->Confirm file format conversion on open http://feedback.mendeley.com/forums/4941-mendeley-feedback/suggestions/1384943-bug-refresh-bibliography-in-word-creates-duplicat
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Remove the first line in Perl $first line…
Remove the first line in Perl $first_line = ; while () { do_something(); }
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Mask repetitive region using BEDtools intersectBed a reads…
Mask repetitive region using BEDtools. intersectBed -a reads.bed -b repeat_region.bed -v
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Viewing huge text files between specific lines $…
Viewing huge text files; between specific lines $ sed -n 101,110p /var/log/cron 10 Awesome Examples for Viewing Huge Log Files in Unix