RNA-seq pipelines (long-, small- and rampage) v2.3.5

All changes contained in this release will produce results that are compatible back to v2.2 (or further).

This release include the following minor change:

Rampage/CAGE pipeline now supports both stranded and unstranded datasets

RNA-seq pipelines (long-, small- and rampage) v2.3.4

All changes contained in this release will produce results that are compatible back to v2.2 (or further).

This release include the following minor change:

1. long-RNA-seq paired-end pipeline now supports both stranded and unstranded datasets

RNA-seq pipelines (long-, small- and rampage) v2.3.3

All changes contained in this release will produce results that are compatible back to v2.2 (or further).

This release include the following minor changes:

1. long-RNA-seq RSEM quantification now includes a ScriptSeq vs. TruSeq parameter.
2. small-RNA-seq STAR alignment now allows for alternate clipping models for ENCODE 2 data.
3. All alignments that concatenate mutiple fastq files, have a better naming scheme for the result.

RNA-seq pipelines (long-, small- and rampage) v2.3.2

This is a pre-release.

This release contains nothing substantially different from v2.3.1. It is being created to tag the latest code before changes to the small-RNA pipeline meant to support ENCODE2 data.

RNA-seq pipelines (long-, small- and rampage) v2.3.1

This release contains a minor fix to rampage-peaks calling. GRIT 2.0.5 fixed a small bug with how the read strands were calculated. While newer results are backward compatible with v2.3.0, rare datasets would fail on peak calling with that version.

RNA-seq pipelines (long-, small- and rampage) v2.2.1

This release contains the cosmetic changes and minor fixes over v2.1.0.

• RSEM has been updated to version 1.2.23

ENCODE_longRNApipeline_v1.1

NOTE: This release had been tagged as ENCODE_longRNApipeline_v2.0 but is really 1.1!

This production release is of the ENCODE long-rna-seq-pipeline version 1.1 as used in https://www.encodeproject.org.
The essential change from release v1.5 is a the STAR tool version is now 2.4.0k, which fixes a problem when processing very large fastq files. Despite the major version number changing, the results of the 2.0 pipeline are expected to be identical to those of v1.5. The reason for the major revision change is that the long-rna-seq-pipeline is now stable and no significant changes are anticipated going forward.

Note:

The small-rna-seq-pipeline, also included in this repository is also substantially finished and no significant changes are anticipated going forward.
The rampage-rna-seq-pipeline is not yet stable and is not in production.

RNA-seq pipelines (long-, small- and rampage) v2.3.0

This release has been superseded by v2.3.1.

This release contains all changes made in preparation for running all three pipelines against GRCh38 human genome. All changes should be backward compatible to the previous (v2.2.0) release.

Specific changes:

• Now using STAR version 2.5.1b. The most notable change is that very last spike-in region had been missing from quantification results but is now being included.
• DX/encodeD independent scripting is separated out (into resources/usr/bin/*.sh) for easier redeployment.

v2.2.3

Did I say star 2.5.1a?  Make that STAR 2.5.1b.

RNA-seq pipelines (long-, small- and rampage) v2.2.2

This release contains all cosmetic fixes prior to v2.3.0