Validate HCA SS2 pipeline for single-end read samples

[kbergin]

Why? The HCA SS2 code has been updated to handle both paired-end and single-end reads. we need to validate the pipeline to make sure it can correctly process both types of data.

Where to start?  Start with the SS2 single-end read samples in the HCA portal and process all samples in a plate (96 or 384 cells). We plan to delegate some of the scientific validation work by seeking opinions on some of the results from the authors who published the data. With suggestions from Ambrose or Tim reach out to the authors for comments on our output

AC: 

• Run the data through the pipeline
• Do a preliminary scientific validity test, such as the right amount of gene counts, biotypes counts, etc
• After discussing with Ambrose or Tim reach out to the authors for comments on the count matrix or other suggestions to make sure the scientific results are sensible.

Ambrose put specific metrics to measure to decide if this validation passes here in a comment.

┆Issue is synchronized with this Jira Dev Task

[kbergin]

whosoever shall pick this up, confirm that the refinement makes sense.

[kbergin]

➤ Nick Barkas commented:

Validation report link: https://docs.google.com/document/d/1MonsTG8UnROHZ_XpulrSZNTxO988KEH6T6h45plFYQg/edit ( https://docs.google.com/document/d/1MonsTG8UnROHZ_XpulrSZNTxO988KEH6T6h45plFYQg/edit|smart-link )

[kbergin]

➤ Nick Barkas commented:

I have done a first pass at reviewing this document. I think there are more improvements to be made, but there are too many open comments and suggestions that make it difficult to read. I would like to review it again when these are addressed / merged.

[kbergin]

➤ Nick Barkas commented:

Reviewed, can be moved to done