Hi there!
I am interested in plants with sex chromosomes. My colleagues would like to see software, where they can put these files as an input:
- file with male reads (father)
- file with female reads (mother)
- many files with male reads (sons)
- many files with female reads (daughters)
(all being Illumina cDNA for example)
and as an output they would get candidate X-linked and Y-linked genes. From few articles I have read about this topic (it's not my area of expertise) I got a feeling, that it's often the series of steps (contig assembly, sorting based on quality, mapping of reads, snp and indel detection..), which could be (hopefully:) simplified to just providing Illumina files and after couple of hours, obtaining candidate X-linked and Y-linked genes (by combing some of already existing tools + processing of results, filtering, formatting..).
Does such software already exist? And in case no, what functionalities would you consider interesting? (This question is sequel of post http://biostars.org/post/show/49689/which-new-bioinformatics-related-tool-would-you-appreciate-the-most/ )
Thanks a lot.
------------------- Experimental design:
- get cDNA reads sequenced with Illumina technology for parent generation of plants (mother and father) and male and female children
- assemble these reads into contigs, so that segments corresponding to individual genes can be identified
- find corresponding genes (one contig for mother, father, every son and every daughter)
- examine differences (snps, indels) and decide which have arisen due to sequencing errors and which correspond to different alleles
- based on these counts (and knowledge of segregation patterns) decide which genes are located on sex chromosomes
- print these candidate X-linked and Y-linked genes
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I think what you mean is a
pipelineto detect such cases. I am not aware of that, but I am guessing this paper which I read recently might interest you. Its on A. thaliana on gene imprinting and allele specific expression.Could you explain a bit more what you mean by X-linked, Y-linked, and what should be in the input files, could this be based on variant calls, for example? Is this human data, and are you therefore interested in alleles on sex-chromosomes only? (Not saying I can help you with this extra information, but maybe others can)
I am interested in alleles on sex-chromosomes only. In order to make analysis as comfortable as possible, I would like to use just raw Illumina cDNA data at the beginning. Then assemble the contigs, find the corresponding ones (for mother, father, children), map reads back to contigs, do variant calling and from number of variants infer if gene could be located on X (Y). I am mainly interested in plants. This tool could therefore be used for our models plants and also for all plant species with sex chromosomes.
Is the issue that your genomes of interest don't have good assembles, and the sex chromosomes are unknown or unassembled? This is the only interpretation of the task that makes sense to me.
If your datasets were phenotypic measurements (for parents and progeny, split by sex), you could go through and assess statistically whether the phenotype showed sex linkage.
However, for genotype information (sequencing data), the only relevant issue for sex linkage is if the allele is on a sex chromosome. For known genomes like humans, this can be done relatively simply via mapping (ignoring hopefully rare issues like sequence regions not present in the reference).
If you are doing this without a reference, you need to get closer to the biology and determine what properties the sex chromosomes will have (copy number specific to gender, etc.). From your original question it sounds like you're focusing on humans, but from your later comment it sounds like plants, so I don't know which direction to go in.
Could it be it's about maize? Just guessing...
Yeah, hard to tell. I don't think maize has X and Y chromosomes, and "fathers and sons" (in the original question) is a bit strange terminology for the plant world (though I guess it could be more metaphorical).
I'm not a plant person, but plant sex determination can be pretty unusual and unlike more familiar species (e.g. with hermaphrodites, etc.), see maybe this paper.
You are right, mother, father terminology is somewhat misleading in this case:( Thanks for the paper, I have not read this particular one (although people here are mostly focused on sex chromosomes:)
Yes, we are talking about plant species that actually don't have any assembles and therefore there isn't any reference sequence available (like Silene for example). I know that only information I get this way is if the allele is on a sex chromosome, but I think this could be enough. Alternatively, as an improvement, I could think about preparing input for commercial software like JoinMap.
What species? What technology and protocol are you using? What is the experimental design? Please edit your question to add these details.
Hi Sean, I added detailes as you proposed.