Commit 0dea3358 authored by Holger Brandl's avatar Holger Brandl

simplified redundant export in kallisto data aggregation

parent 2af95767
......@@ -217,10 +217,7 @@ gene_tpm = tx$abundance %>%
rownames_to_column("ensembl_gene_id") %>%
gather(replicate, tpm_by_gene, - ensembl_gene_id) %>%
tbl_df %>%
left_join(ids, by = "ensembl_gene_id") %>%
select(ensembl_gene_id, ensembl_transcript_id, replicate, tpm_by_gene) %>%
mutate(ensembl_transcript_id = str_replace_all(ensembl_transcript_id, "[.][0-9]*$", ""))
write_tsv(gene_tpm, "tpms_by_geneID.txt")
write_tsv("gene_tpms.txt")
# gene level counts
......@@ -229,10 +226,7 @@ gene_counts = tx$counts %>%
rownames_to_column("ensembl_gene_id") %>%
gather(replicate, count_by_gene, - ensembl_gene_id) %>%
tbl_df %>%
left_join(ids, by = "ensembl_gene_id") %>%
select(ensembl_gene_id, ensembl_transcript_id, replicate, count_by_gene) %>%
mutate(ensembl_transcript_id = str_replace_all(ensembl_transcript_id, "[.][0-9]*$", ""))
write_tsv(gene_counts, "counts_by_geneID.txt")
write_tsv("gene_counts.txt")
## get kallisto count results
......
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