Assembly of transcripts of specific genes from the RNA-seq data
3
1
Entering edit mode
6.9 years ago
vjanousk ▴ 10

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 • 2.8k views
ADD COMMENT
1
Entering edit mode
6.8 years ago
Lior Pachter ▴ 610

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

ADD COMMENT
0
Entering edit mode
6.9 years ago
h.mon 34k

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 COMMENT
0
Entering edit mode

Thanks! It helps.

ADD REPLY
0
Entering edit mode
6.9 years ago
tyler.weirick ▴ 120

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 COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1801 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6