Program introduction
What is Sleuth?
Sleuth is a program that performs differential expression analysis of gene isoforms using the transcript abundance estimates output from alignment-free methods, such as Sailfish, Salmon and Kallisto.
What is wasabi?
Wasabi is a program that converts Sailfish and Salmon output for downstream analysis with Sleuth .
Format conversion
We use Wasabi to prepare Salmon output for downstream analysis with sleuth
Copy $ cd /home/USER/SSAPs
$ R
Define the file path to Salmon (and STAR+Salmon) quant directories
The "Salmon " mapping strategy is described here
The "STAR + Salmon " strategy is described here
The "Salmon with bootstrap " strategy is described here
Copy library (wasabi)
# Salmon
files1 = file.path ( "salmon" , list.files ( "salmon" ))
# STAR + Salmon
files2 = file.path ( "salmon_star" , list.files ( "salmon_star" ))
# Salmon with bootstrap
files3 = file.path ( "salmon-bs" , list.files ( "salmon-bs" ))
Copy > files1
[ 1 ] "salmon/ERR2675454" "salmon/ERR2675455" "salmon/ERR2675458"
[ 4 ] "salmon/ERR2675459" "salmon/ERR2675460" "salmon/ERR2675461"
[ 7 ] "salmon/ERR2675464" "salmon/ERR2675465" "salmon/ERR2675468"
[ 10 ] "salmon/ERR2675469" "salmon/ERR2675472" "salmon/ERR2675473"
[ 13 ] "salmon/ERR2675476" "salmon/ERR2675477" "salmon/ERR2675478"
[ 16 ] "salmon/ERR2675479" "salmon/ERR2675480" "salmon/ERR2675481"
[ 19 ] "salmon/ERR2675484" "salmon/ERR2675485"
> files2
[ 1 ] "salmon_star/ERR2675454" "salmon_star/ERR2675455" "salmon_star/ERR2675458"
[ 4 ] "salmon_star/ERR2675459" "salmon_star/ERR2675460" "salmon_star/ERR2675461"
[ 7 ] "salmon_star/ERR2675464" "salmon_star/ERR2675465" "salmon_star/ERR2675468"
[ 10 ] "salmon_star/ERR2675469" "salmon_star/ERR2675472" "salmon_star/ERR2675473"
[ 13 ] "salmon_star/ERR2675476" "salmon_star/ERR2675477" "salmon_star/ERR2675478"
[ 16 ] "salmon_star/ERR2675479" "salmon_star/ERR2675480" "salmon_star/ERR2675481"
[ 19 ] "salmon_star/ERR2675484" "salmon_star/ERR2675485"
> files3
[ 1 ] "salmon-bs/ERR2675454" "salmon-bs/ERR2675455" "salmon-bs/ERR2675458"
[ 4 ] "salmon-bs/ERR2675459" "salmon-bs/ERR2675460" "salmon-bs/ERR2675461"
[ 7 ] "salmon-bs/ERR2675464" "salmon-bs/ERR2675465" "salmon-bs/ERR2675468"
[ 10 ] "salmon-bs/ERR2675469" "salmon-bs/ERR2675472" "salmon-bs/ERR2675473"
[ 13 ] "salmon-bs/ERR2675476" "salmon-bs/ERR2675477" "salmon-bs/ERR2675478"
[ 16 ] "salmon-bs/ERR2675479" "salmon-bs/ERR2675480" "salmon-bs/ERR2675481"
[ 19 ] "salmon-bs/ERR2675484" "salmon-bs/ERR2675485"
Run the prepare_fish_for_sleuth
function to start conversion
Copy prepare_fish_for_sleuth( files1 )
prepare_fish_for_sleuth( files2 )
prepare_fish_for_sleuth( files3 )
The function will create abundance.h5
files in sleuth-compatible format in the same directory as the Salmon quant.sf
files
Copy > list.files ( file.path ( "salmon" , list.files ( "salmon" )),
full.names = TRUE , pattern = "abundance.h5" )
[ 1 ] "salmon/ERR2675454/abundance.h5" "salmon/ERR2675455/abundance.h5"
[ 3 ] "salmon/ERR2675458/abundance.h5" "salmon/ERR2675459/abundance.h5"
[ 5 ] "salmon/ERR2675460/abundance.h5" "salmon/ERR2675461/abundance.h5"
[ 7 ] "salmon/ERR2675464/abundance.h5" "salmon/ERR2675465/abundance.h5"
[ 9 ] "salmon/ERR2675468/abundance.h5" "salmon/ERR2675469/abundance.h5"
[ 11 ] "salmon/ERR2675472/abundance.h5" "salmon/ERR2675473/abundance.h5"
[ 13 ] "salmon/ERR2675476/abundance.h5" "salmon/ERR2675477/abundance.h5"
[ 15 ] "salmon/ERR2675478/abundance.h5" "salmon/ERR2675479/abundance.h5"
[ 17 ] "salmon/ERR2675480/abundance.h5" "salmon/ERR2675481/abundance.h5"
[ 19 ] "salmon/ERR2675484/abundance.h5" "salmon/ERR2675485/abundance.h5"
Copy > list.files ( file.path ( "salmon_star" , list.files ( "salmon_star" )),
full.names = TRUE , pattern = "abundance.h5" )
[ 1 ] "salmon_star/ERR2675454/abundance.h5" "salmon_star/ERR2675455/abundance.h5"
[ 3 ] "salmon_star/ERR2675458/abundance.h5" "salmon_star/ERR2675459/abundance.h5"
[ 5 ] "salmon_star/ERR2675460/abundance.h5" "salmon_star/ERR2675461/abundance.h5"
[ 7 ] "salmon_star/ERR2675464/abundance.h5" "salmon_star/ERR2675465/abundance.h5"
[ 9 ] "salmon_star/ERR2675468/abundance.h5" "salmon_star/ERR2675469/abundance.h5"
[ 11 ] "salmon_star/ERR2675472/abundance.h5" "salmon_star/ERR2675473/abundance.h5"
[ 13 ] "salmon_star/ERR2675476/abundance.h5" "salmon_star/ERR2675477/abundance.h5"
[ 15 ] "salmon_star/ERR2675478/abundance.h5" "salmon_star/ERR2675479/abundance.h5"
[ 17 ] "salmon_star/ERR2675480/abundance.h5" "salmon_star/ERR2675481/abundance.h5"
[ 19 ] "salmon_star/ERR2675484/abundance.h5" "salmon_star/ERR2675485/abundance.h5"
Copy > list.files ( file.path ( "salmon-bs" , list.files ( "salmon-bs" )),
full.names = TRUE , pattern = "abundance.h5" )
[ 1 ] "salmon-bs/ERR2675454/abundance.h5" "salmon-bs/ERR2675455/abundance.h5"
[ 3 ] "salmon-bs/ERR2675458/abundance.h5" "salmon-bs/ERR2675459/abundance.h5"
[ 5 ] "salmon-bs/ERR2675460/abundance.h5" "salmon-bs/ERR2675461/abundance.h5"
[ 7 ] "salmon-bs/ERR2675464/abundance.h5" "salmon-bs/ERR2675465/abundance.h5"
[ 9 ] "salmon-bs/ERR2675468/abundance.h5" "salmon-bs/ERR2675469/abundance.h5"
[ 11 ] "salmon-bs/ERR2675472/abundance.h5" "salmon-bs/ERR2675473/abundance.h5"
[ 13 ] "salmon-bs/ERR2675476/abundance.h5" "salmon-bs/ERR2675477/abundance.h5"
[ 15 ] "salmon-bs/ERR2675478/abundance.h5" "salmon-bs/ERR2675479/abundance.h5"
[ 17 ] "salmon-bs/ERR2675480/abundance.h5" "salmon-bs/ERR2675481/abundance.h5"
[ 19 ] "salmon-bs/ERR2675484/abundance.h5" "salmon-bs/ERR2675485/abundance.h5"