Hi I am beginner in Bioinformatics and I have recently started working on a project for re-sequencing a whole genome of a black Bengal goat. However, I am struggling to find a certain objective on what we can further work on. We have 4 samples of 10X coverage raw reads and are working on trimming and assembling them.
I have been doing some readings and I am interested in identifying certain genes and their relationship associated with for instance prolificacy or litter size. So far we have found over 10 genes either directly responsible or associated with litter size, but I am lost as to what else can we do? Also I was thinking of study the phylogeny relationships but can I specifically target those genes? We do not have any RNA-seq data and are not currently planning to do so. But can we use SNPs for any sort?
Would really appreciate all the help. I am just an undergraduate so these are fairly new and I am still learning, if you want you can also share some papers where previously did this kind of work.
Thank you in advance!
What kind of reads do you have? RNA?
Usually when you’re resequencing/assembling a genome, that in itself is the point.
Oh thank you for your response. So we have the DNA sequence that we received through illumina sequencing. We have not done RNA seq and have no transcriptome data as well. I am sorry but I couldn't catch what you meant by resequencing being the point.
But you said the project was to resequence the goat genome, is the desired outcome not then a new/better genome assembly?
The most I would think you can do would be variant calling with the new genome, and maybe some comparative genomics with the old assembly to see if you identified anything new of interest.
Its not really the right data to do much functional stuff with, so you won’t be able to push it all that far IMO.
Okay I will try thank you so much!
Is your data Illumina PE short read data ? If so, assembling is not the right word here, I think you have aligned (pls see Wikipedia for the difference) the reads and called SNVs.
I don't know how I would find genes "directly responsible for litter size" from genomic data. Your data will always be correlative (so not direct) and not causal.
There is a tool called PLINK which might help you look at haplotypes and help correlate your data with phenotypes, but I'm not an expert there.
Good luck!
PS - pretty interesting that this is an undergrad project, how times have changed ....