Schumer lab: Where can I find commonly used files

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Which genome assembly and annotation file should I use?

  • For X. birchmanni the current assembly is:

/home/groups/schumer/shared_bin/shared_resources/xiphophorus_birchmanni_10x_12Sep2018_yDAA6.fasta


and the annotation files are:

/home/groups/schumer/shared_bin/shared_resources/Xbirchmanni-10x_12Sep2018_yDAA6-annotation-output


  • For X. malinche the current assembly is:

/home/groups/schumer/shared_bin/shared_resources/xiphophorus_malinche_10x_14Nov2018_HyZ96.fasta


and the annotation files are:

/home/groups/schumer/shared_bin/shared_resources/xiphophorus_malinche_14Nov2018_HyZ96_annotation_output


  • For X. maculatus the current assembly is:

/home/groups/schumer/shared_bin/shared_resources/xma_washu_4.4.2-jhp_0.1_combined-unplaced-mito.fa


and the annotation files are:

/home/groups/schumer/shared_bin/shared_resources/Xiphophorus_maculatus_LG.Xipmac4.4.2.81.gtf

Where can I find i5/i7 barcode files?

Tn5 libraries

For Tn5 libraries, i5 barcode sequences can be found in box under this path:

Schumer_lab_resources/Extractions_and_library_preps/Tn5_i5_indices.xls

For Tn5 libraries, i7 barcode sequences can be found in box under this path:

Schumer_lab_resources/Extractions_and_library_preps/Tn5_i7_indices.xls

Quail libraries

Quail libraries only have an i7 index, which can be found here:

Schumer_lab_resources/Extractions_and_library_preps/Quail_FC1_index_sequence.xls

RNAseq libraries

i5 and i7 indices for kapa RNAseq libraries can be found here:

Schumer_lab_resources/Extractions_and_library_preps/IDX Unique Dual Indexes_forkapa_RNAseq.xls

Which recombination map should I use?

  • The current LD recombination map for X. birchmanni can be found here:


/home/groups/schumer/shared_bin/shared_resources/Xbirchmanni_LD_recombination_map_10xgenome_March2019


  • The current crossover map for F2s can be found here:


/home/groups/schumer/shared_bin/shared_resources/Xbirchmanni_Xmalinche_F2_map_March2019


  • The current crossover map for all artificial hybrids can be found here:


/home/groups/schumer/shared_bin/shared_resources/Xbirchmanni_Xmalinche_all_artificial_hybrids_map_March2019

Where can I find previously run ancestry.tsv files?

Results of previous AncestryHMM runs can be found here:


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


Make sure to put your matching configuration files here too!