Schumer lab: Processed files available on Oak

Previously generated tsv files

Previously generated ancestry tsv files can be found here:

/oak/stanford/groups/schumer/data/Processed_files/Ancestry_tsv_results_files

Remember to put your cfg files in as well with matched names so future lab members can know what parameters were used

Previously generated bam and vcf files

Certain files take a long time to produce and are frequently used by many people in the lab. For this reason we save some processed files on OAK. If you are depositing a file there please make sure it has an informative name. Currently folders containing these types of files included in Processed_files are:

bams_mapped_to_xbir-10x

bams_mapped_to_xbir-pacbio-v2018

bams_mapped_to_xbir-pacbio-v2023

bams_mapped_to_xcor-10x

vcfs_mapped_to_xbir-10x

vcfs_mapped_to_xbir-pacbio-v2018

vcfs_mapped_to_xbir-pacbio-v2023

For more information on the different reference genomes used here please see: https://docs.google.com/document/d/1ztpetGgd2_gwdIhpBQi0MkLhD0u3DbmPSQQyuQeczCY/edit

Cactus alignments

Backups of cactus alignments are available here:

/oak/stanford/groups/schumer/data/Processed_files/cactus_alignments

ABC demographic inference simulated tree files

1 million simulated *.tree files.

/oak/stanford/groups/schumer/data/Processed_files/ABC_simulation_trees/treeFiles/

1,000 sequential trees are compressed and gzipped in finalZippedDirs