Comparing RNA-seq Pipeline Outputs

RNA-seq pipelines commonly produce raw count matrices, normalized expression matrices, and differential expression tables. Compare each artifact with the comparator that matches its scientific meaning.

Counts

pipeconcord compare old/counts.tsv new/counts.tsv --type counts

Use count metrics to check sample-wise correlation, library-size consistency, gene overlap, and zero-pattern agreement.

Normalized Expression

pipeconcord compare old/tpm.tsv new/tpm.tsv --type expression

Use expression metrics to check profile correlation, magnitude similarity, distribution similarity, and top expressed gene overlap.

Differential Expression

pipeconcord compare old/de.tsv new/de.tsv --type deg --alpha 0.05

Use DEG metrics to compare significant gene sets, log-fold-change rank correlation, and up/down direction agreement. Keep contrast direction explicit: flipping the reference condition flips logFC signs.