genomics

Thursday, April 21, 2011

Easing the informatics bottleneck for transcript alignment and assembly for RNAseq data

My new blog post in Scientific Advisory Board..
http://products.scienceboard.net/index.php/archives/2011/04/21/671/
Posted by Sucheta Tripathy PI @ Computational Genomics Group at IICB, Kolkata at 11:53 AM No comments:
Newer Posts Older Posts Home
Subscribe to: Posts (Atom)

Labels

  • Bayesian Probability (1)
  • Contig Assembly (1)
  • Dynamic Programming (1)
  • Heritability (1)
  • Imputation (1)
  • Inteins Exeins (1)
  • N50 (1)
  • Random DNA/Protein Sequence permutation (1)
  • Sequence Alignment (1)
  • Variants (1)

Popular Posts

  • Calculating N50 and L50 of a contig assembly file
    N50 is most often used in draft genome assembly - can be defined as the largest entity E such that at least half of the total size of the...
  • Extracting Fastq files from bam/sam files
    Earlier I have blogged about converting colorspace files into fastq format, which is pretty easy [ here ]. However, this method does not go...
  • Some unix/perl oneliners for Bioinformatics
    1     File format conversion/line counting/counting number of files etc. 1.    $ wc –l   : count number of lines in a file. 2.    $ ls |...
  • Color Space to fastq
    As next generation sequencing is still evolving, so also myriad of tools that are built in and around these sequences . Applied Biosystems D...
  • Calling a perl subroutine from PHP scripts
    I spent a good part of my Christmas vacation in figuring out how to call a perl subroutine from a PHP script . There are several reasons wh...
  • Protein Splicing : Inteins and Exteins
    Protein splicing with inteins(protein introns), exteins(protein exons) was discovered some 20 years ago. Not to mention, this process is eff...
  • Installing Samtools and BEDTools
    Trouble comes as a package when you start your lab. In my effort to resurrect our old database Eumicrobedb.org, I face new challenges every...
  • Plotting Histograms and boxplot with R
    Plotting huge files in R can be a cake walk. Here is how you can proceed: Suppose say you have a huge file with 2 million entries in [TAB...
  • Tool and Paper Watch
    Welcome back! Here I have decided to update the tools available for each of the sections: Genomics; Transcriptomics; Databases; Statistics...
  • To or Not to with cufflink:
    Cufflink is an amazingly easy to install and use software, that lured me into using it. However, it is not without its sets of pitfalls.....

Total Pageviews

Search This Blog

Cluster maps

Locations of visitors to this page

Blog Archive

  • ►  2019 (1)
    • ►  March (1)
  • ►  2013 (6)
    • ►  July (2)
    • ►  June (1)
    • ►  May (1)
    • ►  April (1)
    • ►  March (1)
  • ►  2012 (13)
    • ►  December (1)
    • ►  November (2)
    • ►  August (1)
    • ►  June (2)
    • ►  May (1)
    • ►  April (3)
    • ►  March (1)
    • ►  February (1)
    • ►  January (1)
  • ▼  2011 (15)
    • ►  December (1)
    • ►  October (2)
    • ►  September (4)
    • ►  August (2)
    • ►  July (1)
    • ►  June (1)
    • ▼  April (1)
      • Easing the informatics bottleneck for transcript a...
    • ►  March (1)
    • ►  February (2)
  • ►  2010 (18)
    • ►  November (4)
    • ►  October (1)
    • ►  September (1)
    • ►  August (1)
    • ►  June (1)
    • ►  May (5)
    • ►  April (2)
    • ►  March (3)
  • ►  2009 (26)
    • ►  December (2)
    • ►  October (3)
    • ►  September (1)
    • ►  July (4)
    • ►  April (1)
    • ►  March (5)
    • ►  February (3)
    • ►  January (7)
  • ►  2008 (7)
    • ►  October (6)
    • ►  June (1)
  • ►  2007 (1)
    • ►  March (1)
  • ►  2006 (8)
    • ►  December (1)
    • ►  August (6)
    • ►  June (1)

About Me

My photo
Sucheta Tripathy PI @ Computational Genomics Group at IICB, Kolkata
This is a site to place random thoughts, musings, rantings of my lab members and I.
View my complete profile
Simple theme. Theme images by merrymoonmary. Powered by Blogger.