Citation at end of analysis

[Lioscro]

We should provide a text like this along with the analysis results. Citations should be included for everything.

RNA-seq data was analyzed using Alaska with using the (single, two)-factor design option. Briefly, Alaska performs quality control using BowTie2, etc, etc, etc... and outputs a summary report generated using MultiQC. Read quantification and differential expression analyses of transcripts was performed using Kallisto (v.XXXX) and Sleuth (v.XXXX). Kallisto was run using the following flags: LINE for Single End reads: -b 200, -l (input), -standarddeviationflag (input), -bias

Line for PE reads: -b 200, -bias, - . Reads were aligned using (Species) genome version (version) as provided by Wormbase.

Differential expression analyses with Sleuth were performed using a (LR test or Wald Test) corrected for multiple-testing.

If species == C. elegans: Enrichment analysis was performed using the WormBase Enrichment Suite.

If two-factor design: Alaska performed epistasis analyses as first presented in (cite hypoxia paper).

[Lioscro]

Working on this in branch dev-citation, along with a live view of what commands have been run.

[Lioscro]

33 will be merged soon

[Lioscro]

Sample available here http://alaska.caltech.edu/?id=AP4zl2c5.

[Lioscro]

Implemented in commit 98b660d68ef33b72c734530a32c64411a11a60d2