Question: Hybrid Assembly Transcriptome - Hiseq And 454
2
gravatar for User 8662
8.6 years ago by
User 866220
User 866220 wrote:

hi

i am working on a rna seq dataset which was sequenced PE with 454 and Hiseq. I have assembled 454 with newbler and hiseq using trinity. There is no reference available for the animal which i am working. So i wanted to construct a reference transcriptome using this information. We have lot of coverage more than 30X atleast. What is the best way to use this information to construct reference trascriptome ?

so far with my searching MIRA performs this hybrid assembly but it takes reads and do the assembly. I have the assembled transcripts and i need a pipeline of things i can do to use already assembled transcripts from illumina and 454 and built the reference.

assembly transcriptome • 3.3k views
ADD COMMENTlink modified 5.9 years ago by nehagoel24march0 • written 8.6 years ago by User 866220
1
gravatar for Abhi
8.5 years ago by
Abhi1.5k
United States
Abhi1.5k wrote:

You can try merging the two sets of transcript assembly using PASA. I haven't done this myself but heard about people using PASA to merge overlapping or incomplete transcripts.

You can also look at the RNA-Seq specific section of PASA.

HTH,
-Abhi

ADD COMMENTlink modified 12 months ago by RamRS30k • written 8.5 years ago by Abhi1.5k

I would like to know how to do meta assembly by using the assemblies through Trinity and newbler of Roche transcriptome data. I used CAP3 so I followed the following commands. Both files have different headers and parameters.

cat trinity.fasta newbler.fasta > final.fasta
./cap3 final.fasta

Output: .contigs, .singlets, .ace. links

I think .contigs are assembled and .singlets are unassembled data. Here I don't have .con file as well as I am unable to generate by formcon.

Please guide me how can I get more assembled contigs . Please guide what will be the right way to do.Can you please guide me how the make mira's input to generate meta assembly.

ADD REPLYlink modified 12 months ago by RamRS30k • written 5.9 years ago by nehagoel24march0
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