| """ | |
| AWS Batch wrapper for Luigi | |
| From the AWS website: | |
| AWS Batch enables you to run batch computing workloads on the AWS Cloud. | |
| Batch computing is a common way for developers, scientists, and engineers | |
| to access large amounts of compute resources, and AWS Batch removes the | |
| undifferentiated heavy lifting of configuring and managing the required |
Ensembl's VEP (Variant Effect Predictor) is popular for how it picks a single effect per gene as detailed here, its CLIA-compliant HGVS variant format, and Sequence Ontology nomenclature for variant effects.
To follow these instructions, we'll assume you have these packaged essentials installed:
sudo yum install -y curl rsync tar make perl perl-core
## OR ##
sudo apt-get install -y curl rsync tar make perl perl-base
You'll also need samtools and tabix in your $PATH, which can be found at htslib.org
| #' Convert counts to transcripts per million (TPM). | |
| #' | |
| #' Convert a numeric matrix of features (rows) and conditions (columns) with | |
| #' raw feature counts to transcripts per million. | |
| #' | |
| #' Lior Pachter. Models for transcript quantification from RNA-Seq. | |
| #' arXiv:1104.3889v2 | |
| #' | |
| #' Wagner, et al. Measurement of mRNA abundance using RNA-seq data: | |
| #' RPKM measure is inconsistent among samples. Theory Biosci. 24 July 2012. |
| ## RNA-seq analysis with DESeq2 | |
| ## Stephen Turner, @genetics_blog | |
| # RNA-seq data from GSE52202 | |
| # http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse52202. All patients with | |
| # ALS, 4 with C9 expansion ("exp"), 4 controls without expansion ("ctl") | |
| # Import & pre-process ---------------------------------------------------- | |
| # Import data from featureCounts |
| #!/usr/bin/env python | |
| """ | |
| GTF.py | |
| Kamil Slowikowski | |
| December 24, 2013 | |
| Read GFF/GTF files. Works with gzip compressed files and pandas. | |
| http://useast.ensembl.org/info/website/upload/gff.html |