Hi all,
Has anyone had any issues with SPAdes outputting duplicate sequences between plasmid and chromosome assembly outputs? I have an...
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SPAdes duplicate contigs between chromosome and plasmid
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Using Galaxy Trinity de novo assembly to look for predicted sequence
Hello all,
I am very new to this kind of work and took the time to read through many wikis and methods articles to get to where I am now... -
Issues with bacterial genome assembly (mapping vs. de novo)
I am attempting to assemble a genome from an organism I am working on. Initial BLAST analysis of some assembled contigs has led me to believe I am dealing... -
Program for clustering rna seq reads using protein database
I have an RNA Seq data that I have used to assemble a de novo transcriptome, however, I am having trouble clustering it down into a final set of putative... -
Question about next step in a de novo bacterial genome assembly
I am trying to de novo assemble a large bacterial genome (~9.2MB) with a high GC content (~67%). We have paired end data from a single miSeq run. Using... -
Cleaning up, merging de novo transcriptomes to create a quality reference
Hello,
I have about 950 million reads from an RNA-Seq data set that covers many developmental time-points. Assembling all the reads doesn't... -
De novo RNA-Seq Assembly using Trinity gives too many unigenes.
Hi,
I have done the De novo RNA-Seq Assembly using Trinity with my fish data, but the number of unigenes I get is 333,843, and the N50 Length is... -
Genome guided vs de novo - Trinity
Hi everyone,
For a while now I have been working on my de novo Trinity assembly (fish species). Using my de novo transcriptome I have... -
Best error correction software and methods for de novo assembly of transcriptomes?
Greetings! It seems like a while (5 years) since this question was asked and I am sure there has been lots of progress on the topic in that time. I have... -
How should I parse this blast output?
Hi.
So I have RNA-seq data from a bacteria. I did de novo assembly using the data to create a set of contigs. I then made a blast database... -
Combining >two mappings (reference and de novo) in hexaploid wheat
Hi there,
Has anyone combined more than one mapping data set when analysing with DESeq2 or EdgeR?
We are looking at the interaction... -
PacBio CCS read denovo assambly failed
Hello!
I'm beginning to the field of bioinformatics (I'm 1st year student in bioinformatics and systems biology program) and I got uncorrected... -
genome assembly with only mate pair reads
Hi,
I am mostly comfortable with DNA resequencing, mRNAseq, ChIPseq, etc. data. And always feel difficult handling de novo assembly works.... -
Best way to compare DEG between de novo pipeline and Cufflinks pipeline
Hi!
I would like to know your opinion about WHAT IS THE BEST WAY to compare DEG ( Differentialy Expressed Genes) between de novo pipeline... -
genome comparisons-identifying unique sequences
Hi everyone,
I have assembled de novo the genome of a non model organism, whose female has two strains. My goal is to identify unique sequences...
