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Forum: Bioinformatics 06-26-2014, 01:09 AM
Replies: 0
Views: 1,884
Posted By themysticgeek
Thumbs up Weir And Cockerham Fst from PLINK(bed/bim/fam) input files

I want to calculate markerwise Weir And Cockerham Fst for certain differentiating markers. I have my data in PLINK(bed/bim/fam) format. I have scourged the internet for packages to calculate the fst...
Forum: Bioinformatics 06-08-2014, 10:37 PM
Replies: 0
Views: 1,332
Posted By themysticgeek
What are F2 variants?

The 1000 genomes research article(http://www.nature.com/nature/journal/v491/n7422/full/nature11632.html) studies f2 variants. They refer to these as "Variants present twice across the entire sample...
Forum: Bioinformatics 01-08-2014, 04:42 AM
Replies: 4
Views: 1,901
Posted By themysticgeek
The N's are in ~50% of the reads. I have attached...

The N's are in ~50% of the reads. I have attached the Fasqc image for per base n content. This is particular to this sequening run. Did not observe this problem in the other runs:(...
Forum: Bioinformatics 01-07-2014, 11:07 PM
Replies: 4
Views: 1,901
Posted By themysticgeek
Question How to handle Ns in the middle of reads

For my illumina data fastqc shows presence of N's at positions 13,14,15 in 101 bp longs reads. If i go for cropping first 15 bases by using trimmomatic, it solves the problem but i lose a lot of...
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