Hi, 

I believe a similar question has been asked before ([Question: Is Star Managing Strand-Specific Data ?
][1]), but in the answer to that, it was mentioned that we don't need to do anything extra in STAR alignment if we have strand-aware RNA-seq data. But at another place ([Are any additional parameters for STAR to hand the stranded RNA-Seq data?][2]), the author of STAR mentions that presently STAR doesn't use strand information for mapping, and that if we use a certain option (--quantMode), it provides output for 3 kinds of strandedness). 

So which is it? Does STAR perform strand-aware mapping, which we can use downstream to get antisense transcripts, or if not, then what is the best way to achieve that? I am working with Tru-Seq Stranded Total RNA library, which apparently maps to the opposite strand of the genome (opposite to what you would normally expect).

I am primarily interested in finding novel non-coding transcripts in my data

  [1]: https://www.biostars.org/p/62974/
  [2]: https://groups.google.com/d/msg/rna-star/oGvChGG2gto/UQrP3c8yDQAJ
>strand-aware RNA-seq data

There is no such thing. There are strand-specific library preparations, though, which generate strand-specific (relative to the mRNA) reads, which is probably what you mean.

> Does STAR perform strand-aware mapping, which we can use downstream to get antisense transcripts

You can't get transcripts, sense or antisense - you can get mappings and counts from STAR. What are the downstream analyses you intend to perform?

STAR maps reads to an indexed (most commonly annotated) reference genome, and it doesn't care about transcript strandedness. From these mappings, it can output many different things, which can be used for several downstream analyses. The three most commonly used outputs from STAR are: 

1. read mappings to the genome, in BAM format. By default, strandedness has no importance: STAR maps the reads to the best location, regardless of strand, gene location or whatever. However, the parameter `--outSAMstrandField intronMotif` - **which should be used only if you want to analyse downstream with Cufflinks, and have unstranded RNAseq dara** - alters the default behaviour and adds XS strand attribute. Read the section **Compatibility with Cufflinks/Cuffdiff** from STAR's manual. If you have stranded data, **you don't have to change anything in STAR**.

2. read mappings to the transcriptome, in BAM format. Those are to be used with RSEM, mostly. 

3. counts of reads mapping to genes, similar to HTSeq or featureCounts. Here STAR outputs three columns of counts, one for unstranded, one for stranded, and one for reverse stranded.

Most of these points were already clearly made by Alex Dobin in the thread [Are any additional parameters for STAR to hand the stranded RNA-Seq data?][1], and the STAR manual. 


  [1]: https://groups.google.com/forum/#!msg/rna-star/oGvChGG2gto/UQrP3c8yDQAJ