updating rnaseq data

degron_counts.parquet

@@ -1,3 +1,3 @@
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-oid sha256:b458e1f3388516127832bbd115f2f8567474ad0b795f533fa281a09098695910
-size 95378700
+oid sha256:d9cab86bf569ddcac5a2c984cc73cf7f37bcb5cda3b5e4fcd99dd450865f484d
+size 95464752

mnase_fusion_rnaseq_counts.parquet

@@ -1,3 +1,3 @@
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-oid sha256:bea879d8d2610edaac9153fb0bff49b17ff69a45102be19856a1b5b8dfc2629b
-size 1340335
+oid sha256:a8e0b72f02ec7ce99dbc1fe300678328fba84557a35f1cccf7d4a2a50570a19a
+size 1341547

scripts/dto_preparation.R

@@ -0,0 +1,3 @@
+library(tidyverse)
+library(arrow)
+library(here)

scripts/parse_mahendrawada_rnaseq.R

@@ -7,7 +7,7 @@ names(counts_files) = str_extract(counts_files, "GSM\\d+")
 
 genomic_features = arrow::read_parquet("~/code/hf/yeast_genome_resources/brentlab_features.parquet")
 
-test_count_df = read_tsv(file.path(count_parent_dir, counts_files[[1]]), col_names = c('target_locus_tag', 'count'))
+test_count_df = read_tsv(file.path(count_parent_dir, counts_files[[1]]), col_names = c('orig_locus_tag', 'count'))
 
 find_matching_locus <- function(target, genomic_df) {
     match_idx <- which(str_detect(genomic_df$alias, fixed(target)))
@@ -27,16 +27,29 @@ find_matching_locus <- function(target, genomic_df) {
 }
 
 alias_matched_locus_tags <- test_count_df %>%
+    mutate(target_locus_tag = case_when(
+        orig_locus_tag == "LSR1"  ~ "YNCB0019C",
+        orig_locus_tag == "SCR1"  ~ "YNCE0024W",
+        orig_locus_tag == "snR18" ~ "YNCA0003W",
+        orig_locus_tag == "snR19" ~ "YNCN0005C",
+        orig_locus_tag == "snR3"  ~ "YNCJ0030W",
+        orig_locus_tag == "snR39" ~ "YNCG0014C",
+        orig_locus_tag == "snR4"  ~ "YNCE0019W",
+        orig_locus_tag == "snR5"  ~ "YNCO0028W",
+        orig_locus_tag == "snR6"  ~ "YNCL0006W",
+        orig_locus_tag == "snR8"  ~ "YNCO0026W",
+        .default = orig_locus_tag)) %>%
     left_join(genomic_features,
               by = c('target_locus_tag' = 'locus_tag')) %>%
     filter(is.na(chr), str_detect(target_locus_tag, "^__", negate=TRUE)) %>%
-    select(target_locus_tag) %>%
-    mutate(orig_locus_tag = target_locus_tag) %>%
+    select(orig_locus_tag, target_locus_tag) %>%
     mutate(target_locus_tag = str_replace_all(target_locus_tag, "\\(|\\)", "_")) %>%
     mutate(match_info = map(target_locus_tag, ~find_matching_locus(.x, genomic_features))) %>%
     unnest(match_info) %>%
-    # The following had multiple matches and are determined by hand
-    mutate(target_locus_tag = case_when(
+    select(orig_locus_tag, locus_tag)
+
+locus_tag_map = test_count_df %>%
+    mutate(locus_tag = case_when(
         orig_locus_tag == "LSR1"  ~ "YNCB0019C",
         orig_locus_tag == "SCR1"  ~ "YNCE0024W",
         orig_locus_tag == "snR18" ~ "YNCA0003W",
@@ -47,14 +60,9 @@ alias_matched_locus_tags <- test_count_df %>%
         orig_locus_tag == "snR5"  ~ "YNCO0028W",
         orig_locus_tag == "snR6"  ~ "YNCL0006W",
         orig_locus_tag == "snR8"  ~ "YNCO0026W",
-        .default = target_locus_tag)) %>%
-    select(orig_locus_tag, locus_tag)
-
-locus_tag_map = test_count_df %>%
-    filter(target_locus_tag %in% genomic_features$locus_tag) %>%
-    select(target_locus_tag) %>%
-    dplyr::rename(orig_locus_tag = target_locus_tag) %>%
-    mutate(locus_tag = orig_locus_tag) %>%
+        .default = orig_locus_tag)) %>%
+    filter(locus_tag %in% genomic_features$locus_tag) %>%
+    select(-count) %>%
     bind_rows(alias_matched_locus_tags) %>%
     left_join(select(genomic_features, locus_tag, symbol)) %>%
     dplyr::rename(target_locus_tag = locus_tag,
@@ -286,32 +294,32 @@ metadata_with_counts_meta_with_sample_id$degron =
     dplyr::relocate(sra_accession, gsm_accession,
                     regulator_locus_tag, regulator_symbol)
 
-# for(n in names(metadata_with_counts_meta_with_sample_id)){
-#     meta = list(
-#         path = file.path("/home/chase/code/hf/mahendrawada_2025",
-#                              paste0(n, "_counts_meta.parquet")),
-#         data = metadata_with_counts_meta_with_sample_id[[n]]
-#     )
-#
-#     counts = list(
-#         path = file.path("/home/chase/code/hf/mahendrawada_2025",
-#                              paste0(n, "_counts.parquet")),
-#         data = counts_parsed_list[[n]]$counts
-#     )
-#
-#     arrow::write_parquet(
-#         meta$data,
-#         meta$path,
-#         compression = "zstd",
-#         write_statistics = TRUE)
-#
-#     arrow::write_parquet(
-#         counts$data,
-#         counts$path,
-#         chunk_size = 7036,
-#         compression = "zstd",
-#         write_statistics = TRUE,
-#         use_dictionary = c(
-#             sra_accession = TRUE))
-# }
+for(n in names(metadata_with_counts_meta_with_sample_id)){
+    meta = list(
+        path = file.path("/home/chase/code/hf/mahendrawada_2025",
+                             paste0(n, "_counts_meta.parquet")),
+        data = metadata_with_counts_meta_with_sample_id[[n]]
+    )
+
+    counts = list(
+        path = file.path("/home/chase/code/hf/mahendrawada_2025",
+                             paste0(n, "_counts.parquet")),
+        data = counts_parsed_list[[n]]$counts
+    )
+
+    arrow::write_parquet(
+        meta$data,
+        meta$path,
+        compression = "zstd",
+        write_statistics = TRUE)
+
+    arrow::write_parquet(
+        counts$data,
+        counts$path,
+        chunk_size = 7036,
+        compression = "zstd",
+        write_statistics = TRUE,
+        use_dictionary = c(
+            sra_accession = TRUE))
+}
 

scripts/rnaseq_differential_expression.R

@@ -45,8 +45,7 @@ run_degron_deseq2 <- function(regulator_sym, env_cond, timepoint_val,
         select(target_locus_tag, sra_accession, count) %>%
         pivot_wider(
             names_from = sra_accession,
-            values_from = count,
-            values_fill = 0) %>%
+            values_from = count) %>%
         column_to_rownames("target_locus_tag")
 
     # Create sample metadata
@@ -100,6 +99,8 @@ degron = list(
     meta = arrow::read_parquet("~/code/hf/mahendrawada_2025/degron_counts_meta.parquet")
 )
 
+z = run_degron_deseq2("CYC8", 'standard_30C', 30, degron, baseline_control)
+
 x = map(unique(degron$meta$regulator_symbol),
         ~run_degron_deseq2(., 'standard_30C', 30, degron, baseline_control))
 

wt_baseline_counts.parquet

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-size 1007929
+oid sha256:3cc80db75497486452c4dabbe0b81279577b548c1d0aa0d22898fb98d1e75f22
+size 1008838

wt_degron_control_counts.parquet

@@ -1,3 +1,3 @@
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-size 657259
+oid sha256:3f6c52c34baaf234b6090f5b4bed4fa33d1989ef19c54329b3801def6fb4efb3
+size 657865