Directly reprogrammed myoblasts

  • 30 Jul 2018

    Assembling reads with velvet

    Velvet is a hash-based deBrujin assembler. I occasionally use it to build contigs from short read RNAseq data, although it can be used for long reads, metagenomics, etc. To install, just ...

  • 05 Jul 2018

    GMAP for long read RNA

    GMAP is an old (circa 2006) software for long read alignment. Its use case is for mapping RNA reads back to a genome. It has found new life in the world of long read RNAseq such as from Pacbio ...

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  • 08 Aug

    Using the bioconductor AMI

    The current BioC release is 3.3 for which there is an Amazon AMI (ami-64d43409). I’m not ...

  • 08 Aug

    Setting up AWS CLI

    AWS has a command line interface which may be easier for programmers to use. To set up on a ...

  • 26 Jul

    getting lists of rRNA, miRNA in R

    Recently i had to remove all small RNAs from some cufflinks data. There are lots of way to do ...

  • 26 Jul

    Enable X on AWS EC2 instance

    Spin up an EC2 instance. For this demo, I used an t2.micro instance with the base amazon Linux ...

  • 19 Jul

    Accessing biomart from R

    A good use for Ensembl’s biomart is the ability to pull a list of gene names linked to ...

  • 12 Jul

    How to view function definitions in R (S3/S4)

    Typically, when you type the name of a function in R, it will show you the source code of that ...

  • 23 Mar

    ipython notebooks

    ipython notebooks are a useful way to run/save a session of python code/analysis. I can see it ...

  • 10 Mar

    D3 for visualization

    This uses an older version of D3 (version 3). The concepts are still valid but some of the ...

  • 11 Dec

    Bash shortcuts

    Useful but no well known shortcuts to editing previous commands in bash !! expands to the last ...

  • 16 Nov

    The amazing GNU parallel

    The GNU parallel allows you take advantage of multiple cores on your machine Nice ...

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  • Assembling reads with velvet

    Velvet is a hash-based deBrujin assembler. I occasionally use it to build contigs from short read RNAseq data, although it can be used for long reads, metagenomics, etc. To install, just download, extract and make. There are two parts to the program: 1. velveth – prepare the sequences 2. velvetg – build the graph and...

  • GMAP for long read RNA

    GMAP is an old (circa 2006) software for long read alignment. Its use case is for mapping RNA reads back to a genome. It has found new life in the world of long read RNAseq such as from Pacbio reads. Perhaps because of its age and architecture, it has some quirks and dependencies that seem...

  • Serving BAM files from S3

    Its handy to have a webserver where you can put up BAM files for sharing with collaborators. But if you have tons of files or available webserver, you can use Amazon S3 to serve up your files. While S3 is pretty simple, setting it up for serving BAM (and index) files has a few tricky...

  • Packaging your data in R

    Packaging your data in R The goal of this is to make distribution of your data easy and consistent. The steps are not hard if you are using RStudio. The New Project wizard will do some of the work for you. Create a directory for the R project (myproject) Create a subdirectory (myproject/data-raw) In the...

  • Organizing bioinformatics projects

    I struggle with this all the time. What’s the best way to organize projects? Here’s on suggestion for organizing R from Software Carpentry¬† This is a directory structure I like from an older PLOS paper