'make_fastqs': enable 10x multiome and ATAC Fastq generation to operate with Illumina indexes - #1157
Merged
Merged
Conversation
…dexes. Updates the Fastq generation pipeline to operate with sample sheets that have Illumina barcode indexes (10x indexes also still supported).
…& '10x_multiome_atac' protocols. Updates the Fastq generation pipeline to add support for the '10x_multiome_*' protocols to operate with sample sheets with Illumina index sequences (10x indexes are also still supported).
…mina indexes. Updates the unit tests to include '10_atac', '10x_multiome_gex' and '10x_multiome_atac' Fastq generation protocols with Illumina indexes.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Updates the
10x_multiome_gex,10x_multiome_atacand10x_atacFastq generation protocols (used for 10x Genomics single cell multiome and ATAC data) to operate with Illumina barcode index sequences supplied in the sample sheet, as now recommended by 10x Genomics for these applications.Using the Illumina index sequences mean that the
cellranger-arc mkfastqandcellranger-atac mkfastqcommands are no longer required, however for the time being the 10x Genomics index IDs are also supported by the pipeline (which do still require these packages).Closes #1135.