Greetings.
I have some nice long read data for a diploid animal. There are no references species or even genera in this group and the...
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Computational Karyotyping of non-model species genomes
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differential expression analysis in non-model species - best practice?
Hi All,
I've trawled the forums but have not found a complete discussion around this question: For RNA-seq DE analysis in non-model species,... -
SNP flanking regions with "pseduo"-reference & viewing all alignments around SNPs
Hi everyone,
Sorry for the long post but I could really use your help! I'm trying to verify flanking regions around SNPs and worried about... -
Extracting sex chromosomes from sequenced genomic DNA reads or assembled genome
Hi everyone.
I have two sets of data; male and female (Illumina sequenced, PE reads, ~300 million each, 100bp) of a non-model organism... -
Large discrepancy between de novo assembly versus actual biological genome size
Hello everyone,
I’m in the midst of assembling a eukaryotic genome for the first time, working in a non-model plant species, and I could... -
Best strategy to get GO terms for a proteome?
Hi,
I would like to know the best strategy to get the highest amount of GO terms for the bacterial proteome I'm working. Since it's a non-model... -
Method for targeted sequencing
Hi,
My goal is to obtain the sequence of a gene from several species. I know the sequence only in 2 species separated by ~30mya. Designing... -
Annotating and finding genes of a non-model organism (no reference genome)
I desperately need some help in brainstorming how to approach my data. I have a de novo assembled genome of a non-model organism (no available reference... -
Optimal Insert Length for RNAseq on Illumina?
Hello,
I am planning on using RNAseq with Illumina to generate a de novo transcriptome for a non-model mammal species. I'll be using a... -
Cufflinks non-model organism, issues with -b, and false concatenation of genes
Hello,
I have been working with the "tuxedo" package for a little while now, and have started getting the nice results that I want,...
