Question: Assembly of transcripts of specific genes from the RNA-seq data
1
gravatar for vjanousk
3.7 years ago by
vjanousk10
European Union
vjanousk10 wrote:

Hi,

I have a once produced RNA-seq data of many individuals (~ hundreds) with no reference genome and I am interested only in a subset of transcripts (i.e. transcripts of only a few specific genes). So given the number of individuals the assembly of the whole transcriptomes would be very time consuming. I have been thinking that maybe a subsetting the reads specific for the genes of interests before the actual assembly would be an option. I have been thinking that I could use orthologous sequences of the specific genes of closely related species and for instance bowtie aligner to obtain reads for these genes and then assemble de novo transcripts based on the subset of reads. Do you think this is a good approach? Is there any other approach how to select a subset of reads based on sequence similarity? I appreciate any suggestion. Thanks.

rna-seq assembly • 1.9k views
ADD COMMENTlink modified 2.6 years ago by Biostar ♦♦ 20 • written 3.7 years ago by vjanousk10
1
gravatar for lakigigar
3.6 years ago by
lakigigar220
United States
lakigigar220 wrote:

kallisto is not an assembler, and therefore not directly relevant in this setting.

ADD COMMENTlink written 3.6 years ago by lakigigar220
0
gravatar for h.mon
3.7 years ago by
h.mon24k
Brazil
h.mon24k wrote:

Your approach sounds ok, but either set bowtie to allow a number of mismatches, or use a mapper which allows more divergent reads to align (e.g. Anfo or maybe BBMap). Then assemble, and repeat the alignment step, but using your newly assembled transcripts as reference. You may have to repeat this a number of rounds.

ADD COMMENTlink written 3.7 years ago by h.mon24k

Thanks! It helps.

ADD REPLYlink written 3.7 years ago by vjanousk10
0
gravatar for tyler.weirick
3.7 years ago by
tyler.weirick120
Germany
tyler.weirick120 wrote:

Why not just use one of the faster pseudo-alignment assemblers?  I have heard good things about Kallisto http://pachterlab.github.io/kallisto/ . Supposedly it is like 1000 times faster than a Tophat+Cufflinks assembly. I think there are a number of other fast assemblers like this https://en.wikipedia.org/wiki/List_of_RNA-Seq_bioinformatics_tools

ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by tyler.weirick120

Thanks, Tyler. That sounds like a good option. I'll try that. V.

ADD REPLYlink written 3.7 years ago by vjanousk10
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