Question: Haplotype RNA-seq data
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gravatar for bdeonovic
3.7 years ago by
bdeonovic160
United States
bdeonovic160 wrote:

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

rna-seq haplotype • 1.5k views
ADD COMMENTlink modified 2.9 years ago by colindaven1.2k • written 3.7 years ago by bdeonovic160
0
gravatar for k.rue-albrecht
2.9 years ago by
k.rue-albrecht20 wrote:

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

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by k.rue-albrecht20
0
gravatar for colindaven
2.9 years ago by
colindaven1.2k
Hannover Medical School
colindaven1.2k wrote:

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.

ADD COMMENTlink written 2.9 years ago by colindaven1.2k
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