This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Hybrid Assembly Transcriptome - Hiseq And 454

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
• 4,696 views • link
updated by Nai • Nai • written by User 8662 • User 8662

2 answers

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

• 3 views • link
updated by Ram Ram • written by Abhi Abhi

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.

• 0 views • link
updated by Ram Ram • written by Nai • Nai

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.

• 0 views • link
updated by Ram Ram • written by Nai • Nai

Log in to answer this question.

More posts like this