seq2science

Automated preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows.

• TPM to gene counts conversion with pytxi
  • by default attempts to use the GTF file to convert transcript_ids to gene_names
  • otherwise will use MyGene.info
• config option tpm2counts to chose which TPM to counts converter to use

• pytxi is now the default TPM to gene counts converter (over tximeta)
• peak/gene counts tables now use descriptive names (if given)
• MultiQC DESeq2 correlation plots now display correlation metrics in the figure
• using awful practices to eliminate checkpoint strandedness
• deeptools_flags renamed to deeptools_bamcoverage
• rna-seq trackhub per base tracks by default instead of bins per 50

• edge-cases where seq2science was too strict with rerunning
• assembly stats log scale on the y-axis
• s2s explain wont tell you about subsampling to -1 (all) reads
• tn5 shift cigar string parsing edge-case (reference deletions/insertions)