Busco transcriptome assembly assessment ! would you please suggest the assessment or anything about assembly quality in non-model organisms?

I have paper published (and cited) in Scopus Journal but the citation didn't appear in Google Scholar. How do I link Scopus and Google Scholar?

Hello, for all.

I have papers published at Scopus Journals and I have citation doesn't add yet at Scopus cite.

How can i add its immediately. I need increase my H-index immediately.

Thank you very much for helping me.

How to I add missing citations in my profile on Google Scholar, especially the Chinese citations?

When you assembly a transcriptome with Trinity, for example, only one final fasta is created with the transcriptome. The de novo transcriptome assembly does not assemble transcripts for the separate alleles, and usually there is only one transcript generated and it is mapped to both alleles. Is there any software that allows assembly de novo and with reference genome transcrips for separete alleles?

Hello everyone,

These days I've read many papers regarding RNA-seq and its corresponding analysis, I found when it comes to assembly part, almost every paper would tell how many contigs and scaffolds, which are basically called 'unigenes', have formed out of cleaning reads.

Since I'm not familiar with the assembly process I'm looking on the internet and find a pic elucidating the procedure involved which I've attached below. As in the pic, there are four contigs which comprise two scaffolds, name them as 1,2,3 and 4.

MY QUESTION is first why it cannot be the case that contig 1,2,3 or 4 itself rather than larger sequence (scaffolds) they combined would be recognized as 'unigene'.

Second question would be how to determine which two contigs in the pic comprising scaffolds which represent the real transcriptomes, since basically contig 2 and 3 are also able to be gathered as a scaffold, all of them have certain gaps inbetween.

Many thanks in advance.

Hey all,

I'm trying to identify novel isoforms from MinION Direct RNA sequencing data of mouse samples. My approach so far has been to align reads to genome with Graphmap which gave a good alignment rates and using Pinfish for transcriptome assembly, but my final collapsed transcripts seem to be missing out on a lot of genes from the genome.

Is there a better approach to carry this out to identify novel transcripts, or are there better softwares to carry this out ? I've considered Canu and Masurca but they are not optimizes for RNA reads. Any help would be appreciated !

Thanks,

A

I have RNA-seq data of 2 plant varieties (same species) with 2 developmental stages each. I want to make a transcriptome assembly. What will be the best strategy? 1. Making only one assembly for all reads. 2. Making 2 assemblies for 2 varieties. 3. Making 4 assemblies with each developmental stages.

Consider samples from tissues A and B of a species X collected from geographical location 1 and samples from the same tissues A and B collected from geographical location 2. If we are to do differential expression analysis for all the samples, what will be the best way to generate reference transcriptome assembly? Pooling in reads from all samples together to do one transcriptome assembly OR performing assemblies for each sample separately and then pooling in the non-redundant assembled transcripts? Any other precautionary measures to be taken for such an analysis? Please share references if possible.

Based on the difference between eukaryotic and prokaryotic mRNA, different libraries have to be prepared if people want to get the transcriptome data from mixed tissue of eukaryotic and prokaryotic mRNA.

I was wondering if there are new methods or tech available for getting the eukaryotic and prokaryotic transcriptome data with just one run.