Question: Which transcriptome assembler is recommended for short-read cancer transcriptome data?
0
gravatar for Benedek Dankó
7 weeks ago by
Budapest, Hungary
Benedek Dankó10 wrote:

Hello!

I would like to do a de-novo transcriptome assembly on human control/cancer, short-read RNA-seq datasets. I would like to identify possible unannotated (cancer-specific) transcripts. Which assembler software would you recommend to use in this case?

Our server has 24 cores, 94 Gb RAM, so any softwares like Trinity would not be possible.

ADD COMMENTlink modified 7 weeks ago • written 7 weeks ago by Benedek Dankó10

Trinity is the best, it can reduce memory if you: - run samples separately - use normalization

Alternatively, rnaSPAdes can be used

Also, you can use some strategies to detect novel genes and fused genes using genome alignments.

ADD REPLYlink written 7 weeks ago by JC11k

any softwares like Trinity would not be possible

Trinity needs a GB of RAM per million reads. How many million reads do you have?

ADD REPLYlink written 7 weeks ago by genomax91k

Around 30 million (paired-end) per sample but there are samples with more (eg. 60-70 million).

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by Benedek Dankó10

You should be able to get them to run with hardware you have.

ADD REPLYlink written 7 weeks ago by genomax91k
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