Haplotype RNA-seq data

Question

[bdeonovic]

What software is available for haplotyping transcriptome data (I have RNA-seq data)

Answer 1

[k.rue-albrecht]

10 months later... doesn't look like there's much :/ I was actually Googling this question and ended up here.

I have just learned about MMSEQ (http://bgx.org.uk/software/mmseq.html#note1), but it is based on bowtie, and I am looking for possibly faster alternative (such as STAR or HiSat2) as I will have lots of data and time performance is present among my considerations.

Also, I just spotted GeneiASE myself: http://www.nature.com/articles/srep21134

I should be clear that these are just results of Google searches, I haven't used either, and therefore I cannot recommend either yet.

Best wishes, Kevin

Answer 2

[colindaven]

Phaser is interesting, I have used it and can recommend it. https://github.com/secastel/phaser The haplotypes generated by RNA-seq are of course pretty short.