Getting gene attributes from biomart
Biomart is an Ensembl service for querying and retrieving data. Here I’ll use R/Bioconductor to get gene positions for a list of genes. We basically need a mart object which encapsulates ...
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22 Jul 2020
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21 Jul 2020
Bioconductor and Docker
Dockerizing your bioconductor code is one way to ensure a reproducible workflow. It also enables easier deployment to cloud environments (e.g. AWS Batch) in case you want to scale your analysis. ...
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22 Jul
Getting gene attributes from biomart
Biomart is an Ensembl service for querying and retrieving data. Here I’ll use ...
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21 Jul
Bioconductor and Docker
Dockerizing your bioconductor code is one way to ensure a reproducible workflow. It also ...
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08 Aug
Working with Pacbio IsoSeq data
Overview With its long single molecule reads, Pacbio IsoSeq offers the tantalizing possibility ...
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29 Mar
Favorite atom packages
hydrogen atom-beautify autocomplete-python busy-signal goto-definition highlight-selected ...
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30 Jul
Assembling reads with velvet
Velvet is a hash-based deBrujin assembler. I occasionally use it to build contigs from short ...
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05 Jul
GMAP for long read RNA
GMAP is an old (circa 2006) software for long read alignment. Its use case is for mapping RNA ...
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01 Jun
Serving BAM files from S3
Its handy to have a webserver where you can put up BAM files for sharing with collaborators. ...
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18 Apr
Packaging your data in R
Packaging your data in R The goal of this is to make distribution of your data easy and ...
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15 Jun
Organizing bioinformatics projects
I struggle with this all the time. What’s the best way to organize projects? Here’s ...
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18 May
Rstudio-server over ssh
Rstudio is a great tool but suppose you need to access your work computer to do some work from ...
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Biomart is an Ensembl service for querying and retrieving data. Here I’ll use R/Bioconductor to get gene positions for a list of genes. We basically need a mart object which encapsulates the species, host and database information. Here I’m using the US west coast mirror. This defaults to the current build (GRCh38) of the human...
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Dockerizing your bioconductor code is one way to ensure a reproducible workflow. It also enables easier deployment to cloud environments (e.g. AWS Batch) in case you want to scale your analysis. The official Bioconductor docker containers are hosted on Docker Hub. They are built with Rstudio-server installed so that you can run an interactive analysis....
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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...
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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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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...