Following up on https://github.com/AlexsLemonade/alsf-scpca/pull/162#issuecomment-993945130, I went ahead and ran the two samples we have been using with --sketch mode for alignment, but keeping the --unfiltered mode as that retains the most similarity with Spaceranger. I then added these runs to the existing notebook (in order to not repeat a lot of the same code) and am showing the results grouped by tool + configuration.
The main output that I was interested in here was checking to see if use of --sketch would increase the total counts and number of genes detected/cell observed when quantifying with Alevin-fry and that is in fact the case. The distributions look much more similar to Spaceranger and the plots showing the spots overlaying the tissue look almost identical to Spaceranger. I kept the addition of --sketch pretty simple, as it looks to mostly duplicate the results seen with Spaceranger. However you do still see a small subset of genes that shows higher gene expression in Spaceranger, like we were seeing in selective alignment, but to a lesser degree.
Following up on https://github.com/AlexsLemonade/alsf-scpca/pull/162#issuecomment-993945130, I went ahead and ran the two samples we have been using with
--sketchmode for alignment, but keeping the--unfilteredmode as that retains the most similarity with Spaceranger. I then added these runs to the existing notebook (in order to not repeat a lot of the same code) and am showing the results grouped by tool + configuration.The main output that I was interested in here was checking to see if use of
--sketchwould increase the total counts and number of genes detected/cell observed when quantifying with Alevin-fry and that is in fact the case. The distributions look much more similar to Spaceranger and the plots showing the spots overlaying the tissue look almost identical to Spaceranger. I kept the addition of--sketchpretty simple, as it looks to mostly duplicate the results seen with Spaceranger. However you do still see a small subset of genes that shows higher gene expression in Spaceranger, like we were seeing in selective alignment, but to a lesser degree.This PR is stacked on #162.
The updated html with the new plots can be found here.