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davidaknowles / leafcutter

Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard
http://davidaknowles.github.io/leafcutter/
Apache License 2.0
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genotype file in sQTL analysis #90

Closed CLeib closed 5 years ago

CLeib commented 5 years ago

Hello,

Can someone please advise me how to prepare the VCF genotype file for the sQTL analysis?

Thanks in advance!

goldenflaw commented 5 years ago

See http://fastqtl.sourceforge.net/.

Best, Yang

On Mon, Jan 14, 2019 at 8:36 AM CLeib notifications@github.com wrote:

Hello,

Can someone please advise me how to prepare the VCF genotype file for the sQTL analysis?

Thanks in advance!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/davidaknowles/leafcutter/issues/90, or mute the thread https://github.com/notifications/unsubscribe-auth/AE1pidL_T5zFF9aw3QC0XPc2fBSwmtNdks5vDJXigaJpZM4Z-Xw9 .

CLeib commented 5 years ago

Hi Yang,

Thank you for your reply! I may have misphrased the question. What I meant to ask is how do I get the VCF file in the first place, before preparing it for the sQTL analysis. Is it an output from LeafCutter, or is there some other recommended way of making it from the data?

Thanks again

goldenflaw commented 5 years ago

No, you obtain the VCF files from either calling SNPs using genotyping arrays, DNA-seq, or RNA-seq and imputing.

Best, Yang

On Mon, Jan 14, 2019 at 12:20 PM CLeib notifications@github.com wrote:

Hi Yang,

Thank you for your reply! I may have misphrased the question. What I meant to ask is how do I get the VCF file in the first place, before preparing it for the sQTL analysis. Is it an output from LeafCutter, or is there some other recommended way of making it from the data?

Thanks again

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/davidaknowles/leafcutter/issues/90#issuecomment-454107387, or mute the thread https://github.com/notifications/unsubscribe-auth/AE1piWjvYzMppeDDd9ox-GTkQLL3G_PIks5vDMqIgaJpZM4Z-Xw9 .

CLeib commented 5 years ago

Alright, Thanks