GitHub - SNAnderson/Imprinting2020: Scripts and input files for Anderson 2020 imprinting manuscript

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Name		Name	Last commit message	Last commit date
Latest commit History 7 Commits
B73.v.PH207_features.out.txt		B73.v.PH207_features.out.txt
B73.v.W22_features.out.txt		B73.v.W22_features.out.txt
B73_features_both_contrasts.out.txt		B73_features_both_contrasts.out.txt
B73_filteredTE_combined_attributes_12.20.18.txt.gz		B73_filteredTE_combined_attributes_12.20.18.txt.gz
B73_genes_within_TEs.txt		B73_genes_within_TEs.txt
B73v4_slimGO.txt		B73v4_slimGO.txt
PHE1_binding_sites_genesTEs.txt		PHE1_binding_sites_genesTEs.txt
README		README
W22.v.PH207_features.out.txt		W22.v.PH207_features.out.txt
ase_1Oct19.rds		ase_1Oct19.rds
batista_motifs_fimo_gene_out.txt		batista_motifs_fimo_gene_out.txt
batista_motifs_fimo_out.txt		batista_motifs_fimo_out.txt
combine_count_tables_input_command_line.pl		combine_count_tables_input_command_line.pl
combined_counts_all_concatinated_genomes_21Oct19.txt.gz		combined_counts_all_concatinated_genomes_21Oct19.txt.gz
concat_3pairs.sh		concat_3pairs.sh
cpm.rds.gz		cpm.rds.gz
element_combined_counts_DevREDO_11Oct19.txt.gz		element_combined_counts_DevREDO_11Oct19.txt.gz
gene_model_xref_v4c.txt		gene_model_xref_v4c.txt
imprint_concat_BP.sh		imprint_concat_BP.sh
imprint_concat_BW.sh		imprint_concat_BW.sh
imprint_concat_WP.sh		imprint_concat_WP.sh
imprint_samples.txt		imprint_samples.txt
imprinting_github.Rmd		imprinting_github.Rmd
imprinting_github.nb.html		imprinting_github.nb.html
matTE_closest_gene_v2.txt		matTE_closest_gene_v2.txt
non-redundant_TEs_by_annotation_4genomes_3May20.txt.gz		non-redundant_TEs_by_annotation_4genomes_3May20.txt.gz
non-redundant_TEs_by_annptation_4genomes_24Jan20.txt.gz		non-redundant_TEs_by_annptation_4genomes_24Jan20.txt.gz

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# Concatenate genomes
qsub /home/springer/sna/scripts/shell/concat_3pairs.sh

# Map reads to concatenated genomes
qsub -t 2,3,4,14,15,16 -v LIST=imprint_samples.txt   /home/springer/sna/scripts/shell/imprint_concat_BW.sh
qsub -t 11,12,13,17,18,19 -v LIST=imprint_samples.txt   /home/springer/sna/scripts/shell/imprint_concat_WP.sh
qsub -t 5-10 -v LIST=imprint_samples.txt   /home/springer/sna/scripts/shell/imprint_concat_BP.sh

# Combined mapped reads
perl /home/springer/sna/scripts/combine_count_tables_input_command_line.pl counts_BW_endo1_to_BW_concat.txt counts_BW_endo2_to_BW_concat.txt  counts_BW_endo3_to_BW_concat.txt  counts_WB_endo1_to_BW_concat.txt counts_WB_endo2_to_BW_concat.txt  counts_WB_endo3_to_BW_concat.txt counts_BP_endo1_to_BP_concat.txt counts_BP_endo2_to_BP_concat.txt  counts_BP_endo3_to_BP_concat.txt  counts_PB_endo1_to_BP_concat.txt counts_PB_endo2_to_BP_concat.txt  counts_PB_endo3_to_BP_concat.txt counts_WP_endo1_to_WP_concat.txt counts_WP_endo2_to_WP_concat.txt  counts_WP_endo3_to_WP_concat.txt  counts_PW_endo1_to_WP_concat.txt counts_PW_endo2_to_WP_concat.txt  counts_PW_endo3_to_WP_concat.txt 

# Add header
echo -e "ID\tBW1\tBW2\tBW3\tWB1\tWB2\tWB3\tBP1\tBP2\tBP3\tPB1\tPB2\tPB3\tWP1\tWP2\tWP3\tPW1\tPW2\tPW3" | cat - combined_counts.txt > ~/te_expression/imprinting/combined_counts_all_concatinated_genomes_21Oct19.txt


# Downstream analysis performed in R. See R notebook for analysis
imprinting_github.Rmd

# Output tables
B73_features_both_contrasts.out.txt - Imprinting calls and attributes for B73 genes and TEs that were assessed for imprinting in either B73 x W22 or B73 x PH207 cross
B73.v.W22_features.out.txt - Output from DESeq from B72 x W22 cross combined with RER values and filtered imprinting calls
B73.v.PH207_features.out.txt - Output from DESeq from B72 x PH207 cross combined with RER values and filtered imprinting calls
W22.v.PH207_features.out.txt - Output from DESeq from W22 x PH207 cross combined with RER values and filtered imprinting calls

# For files needed to create Figure 1C, see https://github.com/kmhiggins/Imprinting_2020