v0.4

rerelease for DOI

v0.4

[0.4] - 2018-12-19

Added

• Top barcode detection using umi-tools based on number of expected cells.
• Genome reference and annotation automatically downloaded now base on build and release number from configuration file.
• On the fly detection of mixed experiment.
• beta: Generation of a report for publication describing tools used in each steps. run make_report after the preprocessing is done to get reports/publication_text.html. This is a really early stage. Feel free to suggest PR for text modifications.
• Raw data, results, reference are now independent from the working dir and can be chosen via the configuration file.
• dropseq_tools v2.0 implemented. This opens up new options such as choosing which locus to use for gene counting. See configuration file.
• Possibility to edit which biotypes are selected from the annotation file via a gtf_biotypes.yaml file provided.
• Cell barcodes are now corrected. One hamming distance for known/given whitelists, graphbased correction based on umi-tools for unknown lists. Those corrections are written in the bam files. This makes final bam files compatible for other tools using the XC/XM bam TAGS.
• UMI are now also corrected based on dropseq_tools v2.0.
• Possibility to choose SENSE, ANTISENSE or BOTH for read counting.
• Adapter content for R1 and R2 have now their own plot, adapter_content.pdf.
• New plot called yield.pdf makes a summary of total reads and how they are distributed among filtered, trimmed, mapped, etc.
• Configuration file has now a CONTACT section providing a field for a person and a contact e-mail address.

Changed

• Expression matrices output are now sparse (mtx format). This will decrease the size of the output and loading time for downstream analysis.
• Logfiles, plots and samples output are now grouped together in folders by category. This should make browsing results easier.
• Fixed most of the packages versions.
• Summary plots and Seurat object are now in the all rule and will be created by default.

Removed

• Merging of species expression accross samples. Since the mixed experiments are mostly used to test out the doublet rate of a platform and not for downstream analysis, this last part has not been updated. Single expression matrices are still there.
• Cell barcodes dropped, umi barcodes dropped, starttrim and polyA trim plots are now gone. BC_drop is also removed. Replacements are adapter_content and yield plots.

Version 0.31

See CHANGELOG for infos about this release