Directly reprogrammed myoblasts

  • 08 Aug 2019

    Working with Pacbio IsoSeq data

    Overview With its long single molecule reads, Pacbio IsoSeq offers the tantalizing possibility of reading entire full-length RNAs. The library prep is not for the faint of heart and a recent ...

  • 29 Mar 2019

    Favorite atom packages

    hydrogen atom-beautify autocomplete-python busy-signal goto-definition highlight-selected linter-flake8 markdown-writer minimap python-autopep8 symbols-tree-view script ftp-remote-edit

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  • Working with Pacbio IsoSeq data

    Overview With its long single molecule reads, Pacbio IsoSeq offers the tantalizing possibility of reading entire full-length RNAs. The library prep is not for the faint of heart and a recent provider asked me for 5ug of RNA to start – not an easy task! Moreover, a thorough interrogation of a transcriptome would require at...

  • Favorite atom packages

    hydrogen atom-beautify autocomplete-python busy-signal goto-definition highlight-selected linter-flake8 markdown-writer minimap python-autopep8 symbols-tree-view script ftp-remote-edit

  • 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...