Suggestion for de novo transcriptome assembly of a plant with high heterozygosity · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

Suggestion for de novo transcriptome assembly of a plant with high heterozygosity

Hi all,

I've got Illumina sequencing reads (100 bp, PE) from a non-model dioecious plant (two genotypes, one is sensitive to treatment and another is tolerant) with high heterozygosity. What's your suggestion for de novo transcriptome assembly and RNA-seq analysis given the high heterozygosity of sample? Is it better to pool all reads or using separate reads from two genotypes for de novo assembly? Thanks for your comments

rna-seq assembly sequencing

• 1,952 views • link

written 10.9 years ago by seta

0 answers

No answers yet.

Log in to answer this question.

More posts like this

Please help me with the issue on FPKM value calculation and validation of transcriptome assembly
written 10.2 years ago by seta

Hi all, I have done a de novo transcriptome assembly and annotation for a non-model plant. For generating a robust assembly, the equal amount of …
Any experience with scaffolding using SSPACE tool
written 10.8 years ago by seta

Hi all, I made de novo transcriptome assembly using about 300 millions PE reads (100bp from Illumina) with different k-mers. Several assembled transcriptome was merged …
why capt3 tool cannot efficiently find the overlapping contigs?
written 11.0 years ago by seta

<p>Hi all,</p> <p>I did transcriptome assembly on illumina PE, 100 bp reads at different k-mers, and now try to merge resulting assemblies. So, I pool …
Using generated transcriptome assembly by two assemblers
written 11.1 years ago by seta

<p>Dear all,</p> <p>I performed de novo transcriptome assembly for a non-model plant using two assemblers, CLC genomic workbench and Trinity tool. Both assembly sounds good, …
How compare two de novo assembled transcriptomes of the same sample with different sequencing depth?
written 11.2 years ago by seta

Hi everybody, I got **two sequencing dataset **derived from sequencing of **one sample** with **two different sequencing depth**, actually, one dataset is composed of about …
How efficiently to use information of two de novo assembled transcriptome for further analysis?
written 11.2 years ago by seta

Hi everybody, I'm working on RNA-seq analysis of non-model plant, my focus is on the root so the extracted RNA from roots of interest under …
How efficiently to use information of two de novo assembled transcriptome for further analysis?
written 11.2 years ago by seta

Hi everybody, I'm working on RNA-seq analysis of non-model plant, my focus is on the root so the extracted RNA from roots of interest under …
High quality de novo transcriptome assembly rely on merging multiple assembly?
written 11.5 years ago by seta

Dear all, Please let me know your experience regarding combining multiple assembly (derived from different k-mer or different programs) to make the** best de novo …
how many RAM and CPU are required to perform comprehensive NGS analysis?
written 11.6 years ago by seta

<p>Hi all,</p> <p>Please provide me how many RAM (GB) and CPU are required to perform de novo transcriptome assembly for about 400 million paired-end reads …
The best factors to evaluate the quality of de novo transcriptome assembly
written 11.7 years ago by seta

Hi everybody, There are different criteria to evaluate de novo transcriptome assembly quality, which all of them have their pros and cons. What are the …