Entering edit mode
12 weeks ago
umeshtanwar2
▴
30
Dear all,
I am working on Lupinus albus plant species and I have Genotyping-by-Sequencing (GBS) data. I have a question about the filtering the SNPs. What decay of linkage disequilibrium (LD) value I should use, in the previously published paper 3.85kb was used. If I use this value It returns millions of SNPs. Can anyone please help.
Thank you
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Transcriptome sequencing platform RNA-Seq Differential gene expression Differential gene expression analysis by DESeq2 Running GSEA for DEGs DESeq2: Differential gene expression Differential gene expression by DESeq2 STAR for Genome Index and Alignment
Using values found in the literature is a good start. What confuses me is why you are uncertain due to the number of SNPs. 1 million is on the smaller side of totals for datasets I'm used to reading, but by no means a bad number.
Do you think this is too many, too little, and why?