I have multiple BAM files to run on feature count. I have tried data collection mode as well as multiple file mode. i want single file with counts from all the samples for DESeq2 analysis. Currently i am getting separate files for for each sample. Kindly guide
Welcome @Vinay_Jain
Hopefully we can help!
Featurecounts always outputs one count file per sample. The same count files can be used multiple ways depending on how the downstream tool consumes the data.
If you plan to use DESeq2, then one count file per sample is the required input format. Scroll down on the tool from to find this description.
Help
Inputs
Count Files
DESeq2 takes count tables generated from featureCounts, HTSeq-count or StringTie as input. Count tables must be generated for each sample individually.
How to process
You can filter your original collections processed through the upstream mapping/counting steps into different collections for the downstream DE analysis. You will need one collection per Factor level.
- Hands-on: Using dataset collections / Using dataset collections / Using Galaxy and Managing your Data (filter-collection)
Or, you can apply group tags to the collection and use the tool that way. We have an example for applying and using group tags here:
- Hands-on: Group tags for complex experimental designs / Group tags for complex experimental designs / Using Galaxy and Managing your Data (using-group-tags-in-tool-eg-deseq2)
If you plan to use Limma instead, then a count matrix will be used. The matrix is created from the individual count files. We have an example in this protocol in this tutorial:
- Hands-on: 1: RNA-Seq reads to counts / 1: RNA-Seq reads to counts / Transcriptomics (create-count-matrix)
Links to more help for similar protocols, and links to workflows, can be found at:
- Help with RNA Star, Featurecounts, and reference annotation choices - #2 by jennaj
- and featurecounts deseq2 limma_voom
With production quality workflows available at the 
IWC Workflow Library. These can be useful resources even if you do not plan on using the entire workflow. Import to review how the data is manipulated, or edit the workflow down to what you need!
- Intergalactic Workflow Commission (q=rna-seq)
Please let us know if this help or if you have follow up questions! 