Using Salmon outputs from Galaxy

[Matthew Brook]

Hi

I love the idea of this workflow. Thanks for all your hard work......

However, I can NOT get the web version to accept my Salmon outputs generated in Galaxy. I have tried LOTS of different ways of formatting the data etc but it just can't seem to get past the fact that Galaxy doesn't give you quant.sf-type files..........

Please can you provide a workaround that allows us to upload Salmon data in a CSV (or other tabular format), as outputted from Galaxy?

This will be HUGELY appreciated.

Many thanks

Matt Brook

[wenbin guo]

Dear Matt,

Many thanks for using our 3D RNA-seq App.

The quant.sf file in a separate folder for each sample of quantification is the standard output of salmon tool. This format is the start point of many RNA-seq expression analysis pipeline, e.g. edgeR and limma. I suppose to make the salmon quantification outputs easy to be used by biologists, the guy who built the quantification pipeline in the Galaxy has added some function to convert the quant.sf file to csv file. Actually, the quant.sf is tab delimited format file, just like a file with .txt extension. Here is my solution for your issue:

1. Prepare the metadata table and include a column of quantification folder names (you can create the names according to your sample information).

2. Create folders according to the quantification folder names in your metadata table

3. For each sample of quantification, open the quantification csv/tabular file in excel. The table should include columns of Name, Length, EffectiveLength, TPM and NumReads if it is salmon output.

4. Click save as to save the table as “Text (Tab delimited) (*.txt)” with a file name quant.txt to a corresponding folder you’ve created in step (2).

5. Now you have quant.txt files in all the corresponding folder. Then you manually change the extension “.txt” to “.sf”. 

6. Now you have quant.sf files in all the corresponding folder of quantification. Then you can prepare the input files according to the user manual https://github.com/wyguo/ThreeDRNAseq/blob/master/vignettes/user_manuals/3D_RNA-seq_App_manual.md#input-files and perform 3D analysis.

If your problem still not get solved, please let me know. 

Best,

Wenbin