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2.1 years ago
Fizzah
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30
Hello there! I want to map local cotton cultivar (which I sequenced) with jin 668 cultivar. But due to limited funding I could not get seeds and perform RNA-sequencing. Is there any alternative method to find Jin668 genome sequence for mapping.. I have consulted a paper in which they performed RNA seq of JIN668 . All sequence data reported in this manuscript can be found in the NCBI sequence read archive (SRA) under BioProject study PRJNA747913 (Samples: SRR15186777- ARR15186784). Please guide how can I retrieve data for mapping from this above mentioned link.
Yes, if raw RNA-seq data are public in SRA you can and may download them with SRA tools and create a transcirptome assembly using e.g. trinity. If no genomic data are available (you need to investigate that) you will unfortunately not be able to reconstruct the genome. You might however find the sequence of a different cultivar and then do a genome-guided transcriptome assembly.
Your example is exactly the reason why we need open data and insist on making data available in a public repository. You could check if there is a public assembly already, then you can also save the assembly step.
Ok thank you soo much.. I will check it
There is a RefSeq chromosome level genome of cotton. I would use that as a reference to call variants from your data.
There are 5 bioprojects for jin668 cultivar in NCBI at this time: https://www.ncbi.nlm.nih.gov/bioproject/?term=cotton%20jin668
At least one appears to be a RNAseq dataset. It is not clear what kind of sequence you have? Do you have genome sequence that you want to map against a transcriptome?
I have a transcriptomic data of my local cotton cultivar that I want to map
While you could try and assemble a transcriptome or a genome of the jin668 cultivar using the raw data from one of the projects above, easiest thing may be to use the model genome that Michael Dondrup linked above. That should give you usable data in terms of what genes are expressed in your sample.