adomingues

Session info ------------------------------------------------------------------
 setting  value                       
 version  R version 3.5.1 (2018-07-02)
 system   x86_64, linux-gnu           
 ui       X11                         
 language en_US                       
 collate  en_US.UTF-8                 
 tz       Europe/Berlin               
 date     2018-08-15                  

adomingues

> devtools::session_info()
Session info ------------------------------------------------------------------
 setting  value                       
 version  R version 3.4.3 (2017-11-30)
 system   x86_64, linux-gnu           
 ui       X11                         
 language en_US:en                    
 collate  en_US.UTF-8                 
 tz       Europe/Berlin               
 date     2018-08-15                  

adomingues

#pip install --user bitbucket-cli
proj="some_project"
bitbucket create --private --protocol ssh --scm git ${proj}
git remote add origin https://adomingues@bitbucket.org/adomingues/${proj}.git
git push --set-upstream origin master

adomingues

ftargets="targets.txt"
fcontrasts="contrasts.txt"
mmatrix="~group"
filter.genes=TRUE
prefix=""
suffix=".raw_readcounts.tsv"
cwd="results/subread-count_MM"
out="results/DE_DESeq2_MM"
gene.model="/fsimb/common/genomes/caenorhabditis_elegans/ensembl/WBcel235/full/annotation/Caenorhabditis_elegans.WBcel235.84.gtf"

adomingues

# resource: http://seqanswers.com/forums/showthread.php?t=4914
# Calculate length for each transcript for a GTF file
awk -F"\t" '
$3=="exon" 
    {
        ID=substr($9, length($9)-16, 15); 
        L[ID]+=$5-$4+1
    } 
END{
    for(i in L)

adomingues

R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

Matrix products: default
BLAS: /usr/lib/atlas-base/libf77blas.so.3.0
LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              

adomingues

## 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

adomingues

Whilst running a `RIPSeeper` analysis, I noticed that the dataset `drerio_gene_ensembl` which used to be available via `biomaRt` is not longer listed or accessible. To test this I first upgraded my `bioC` to make sure I am working with the latest version of `biomaRt` (2.34.0).

```{r update, eval=FALSE}
biocLite("BiocUpgrade")
biocLite("BiocUpgrade")

```

I then followed the instructions in the [vignette](https://bioconductor.org/packages/release/bioc/vignettes/biomaRt/inst/doc/biomaRt.html) and connected to `ensembl`:

adomingues

 setting  value                       
 version  R version 3.4.1 (2017-06-30)
 system   x86_64, linux-gnu           
 ui       X11                         
 language en_US:en                    
 collate  en_US.UTF-8                 
 tz       Europe/Berlin               
 date     2017-11-30                  

adomingues

# A function (borrowed from the Sleuth documentation) for connecting Ensembl transcript names to common gene names
convert_tx_to_gene <- function(dat="drerio_gene_ensembl"){
    mart <- biomaRt::useMart(
        biomart = "ensembl",
        dataset = dat
    )
    t2g <- biomaRt::getBM(
        attributes = c("ensembl_transcript_id", "ensembl_gene_id", "external_gene_name"),
        mart = mart