Question: Genome assembly with RNA-seq data?
0
gravatar for Buffo
2.4 years ago by
Buffo1.2k
Buffo1.2k wrote:

Hi everybody, I have reads from transcriptome and the reference genome, but the reference is fragmented (more than 20k contigs), Somebody knows if is possible to improve the genome assembly using the RNA-SEQ reads? I`m sure that it is not possible with IDBA, SOAP and SPADES Thanks!

ADD COMMENTlink modified 2.4 years ago by h.mon22k • written 2.4 years ago by Buffo1.2k

You may be able to improve local regions with RNAseq reads but chances of finding spanning reads (to bridge contigs, assuming you have paired-end transcriptome reads) would be smaller. Even if you do find them there would be no way to fill the sequence in between.

ADD REPLYlink written 2.4 years ago by genomax60k

Since the reference is that fragmented I guess it can help bridging contigs, correctly orientating them, but indeed the sequence in between will not be filled in.

ADD REPLYlink written 2.4 years ago by WouterDeCoster35k
1
gravatar for h.mon
2.4 years ago by
h.mon22k
Brazil
h.mon22k wrote:

Some papers on the subject: one, two, three.

ADD COMMENTlink written 2.4 years ago by h.mon22k

Thank you so much :-)

ADD REPLYlink written 2.4 years ago by Buffo1.2k
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