New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

mouse genome.fa for step 42 #3

Open

fgv2104 opened this issue Mar 7, 2024 · 0 comments

fgv2104 commented Mar 7, 2024

We are trying to generate a masked genome fasta file for mouse using version 2 of CellRanger-ATAC and we had a few questions on how to achieve this:

-Did you use ensembl to get the fasta files needed for the pre-built blacklist bedfiles?
-Which reference version did you use for mm10?
-Would we then use this file (https://ftp.ensembl.org/pub/release-111/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.primary_assembly.fa.gz) for step 42?
-Do we need to include the input_motifs line in the config.json file in https://github.com/caleblareau/mgatk/wiki/Increasing-coverage-from-10x-processing ?

Thank you for your help!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment