RELEASEnotes

STAR 2.4.2a 2015/06/19

New features:

Counting reads per gene while mapping with --quantMode GeneCounts option.
A read is counted if it overlaps (1nt or more) one and only one gene. Both ends of the paired-end read are checked for overlaps.
The counts coincide with those produced by htseq-count with default parameters.

Requires annotations (GTF or GFF with --sjdbGTFfile option) used at the genome generation step, or at the mapping step.

Outputs read counts per gene into ReadsPerGene.out.tab file with 4 columns which correspond to different strandedness options:
column 1: gene ID 
column 2: counts for unstranded RNA-seq
column 3: counts for the 1st read strand aligned with RNA (htseq-count option -s yes)
column 4: counts for the 2nd read strand aligned with RNA (htseq-count option -s reverse)
Select the output according to the strandedness of your data.
Note, that if you have stranded data and choose one of the columns 3 or 4, the other column (4 or 3) will give you the count of antisense reads.
 
With --quantMode TranscriptomeSAM GeneCounts, and get both the Aligned.toTranscriptome.out.bam and ReadsPerGene.out.tab outputs.



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STAR 2.4.1a 2015/04/17

New features:

1. The annotations can now be included on the fly at the mapping step, without including them at the genome generation step.
   At the mapping step, specify --sjdbGTFfile /path/to/ann.gtf and/or --sjdbFileChrStartEnd /path/to/sj.tab, as well as --sjdbOverhang, and any other --sjdb* options.
   The genome indices can be generated with or  without another set of annotations/junctions. In the latter case the new junctions will added to the old ones.
   STAR will insert the junctions into genome indices on the fly before mapping, which takes 1~2 minutes.
   The on the fly genome indices can be saved (for reuse) with "--sjdbInsertSave All", into _STARgenome directory inside the current run directory.
   Default --sjdbOverhang is now set at 100, and does not have to be specified unless you need to change this value.

   The "all-sample" 2-pass method can be simplified using this on the fly junction insertion option: 
   (i) run the 1st pass for all samples as usual, with or without annotations
   (ii) run 2nd pass for all samples, listing SJ.out.tab files from all samples in --sjdbFileChrStartEnd /path/to/sj1.tab /path/to/sj2.tab ...

2. New option to activate on the fly "per sample" 2-pass method: "--twopassMode Basic".
   Default --twopass1readsN is now -1, i.e. using all reads in the 1st pass.
   2-pass mode can now be used with annotations, which can be included either at the run-time (see #1), or at the genome generation step.
   Annotated junctions will be included in both the 1st and 2nd passes.

3. Included link (submodule) to Brian Haas' STAR-Fusion code for detecting fusion transcript from STAR chimeric output:
   https://github.com/STAR-Fusion/STAR-Fusion

4. Included Gery Vessere's shared memory implementation for POSIX and SysV. 
   To compile STAR with POSIX shared memory, use `make POSIXSHARED`

5. New option "--chimOutType WithinBAM" to include chimeric alignments together with normal alignments in the main (sorted or unsorted) BAM file(s).
   Formatting of chimeric alignments follows the latest SAM/BAM specifications. Thanks to Felix Schlesinger for thorough testing of this option.

6. New option "--quantTranscriptomeBan Singleend" allows insertions, deletions ans soft-clips in the transcriptomic alignments, which can be used by some expression quantification software (e.g. eXpress). 
   
7. New option "--alignEndsTypeExtension Extend5pOfRead1" to enforce full extension of the 5p of the read1, while all other ends undergo local alignment and may be soft-clipped.