# Convert Salmon output to Sleuth-compatible format ## Program introduction ### What is Sleuth? [Sleuth](http://pachterlab.github.io/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](https://github.com/COMBINE-lab/wasabi) is a program that converts Sailfish and Salmon output for downstream analysis with [Sleuth](http://pachterlab.github.io/sleuth/). ## Format conversion We use [Wasabi](https://github.com/COMBINE-lab/wasabi) to prepare Salmon output for downstream analysis with [sleuth](https://github.com/pachterlab/sleuth) ```bash $ cd /home/USER/SSAPs $ R ``` Define the file path to Salmon (and STAR+Salmon) quant directories * The "**Salmon**" mapping strategy is described [here](https://ycl6.gitbook.io/guide-to-rna-seq-analysis/raw-read-processing/mapping/alignment-free-method#salmon) * The "**STAR + Salmon**" strategy is described [here](https://ycl6.gitbook.io/guide-to-rna-seq-analysis/raw-read-processing/mapping/alignment-based-method#star-salmon-quantification-alignment-based-mode) * The "**Salmon with bootstrap**" strategy is described [here](https://ycl6.gitbook.io/guide-to-rna-seq-analysis/raw-read-processing/mapping/alignment-free-method#salmon-with-bootstrap) ```r 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")) ``` ```r > 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 ```r 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 ```r > 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" ``` ```r > 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" ``` ```r > 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" ``` --- # 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