User: gkuffel22

gravatar for gkuffel22
gkuffel2230
Reputation:
30
Status:
New User
Location:
United States
Website:
http://ssom.luc.edu/ge...
Last seen:
an hour ago
Joined:
2 years, 11 months ago
Email:
g********@gmail.com

I am the Laboratory Manager of the Loyola Genomics Core Facility. We have 2 MiSeqs and offer 16S, RNA-Seq, miRNA-Seq, WGS and Targeted Panels. I am also heavily involved with analyzing the data that is generated. 

Posts by gkuffel22

<prev • 27 results • page 1 of 3 • next >
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Comment: C: Getting Haplotypes from a VCF file
... Do you have any information on my actual question about haplotypes? ...
written 8 days ago by gkuffel2230
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Comment: C: Getting Haplotypes from a VCF file
... So I should paste like this for next time? #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 10 110_S24_L001 111_S25_L001 115_S26_L001 118_S27_L001 11_S5_L001 120_S28_L001 121_S29_L001 123_S30_L001 124_S31_L001 12$ gi|1209890|gb|U47338.1|CFMHCDRB02 7 ...
written 8 days ago by gkuffel2230 • updated 8 days ago by Ram13k
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Comment: C: freebayes haplotype calling (phased variants)
... Thank you for the reply. I have 250 bp paired end reads and my user (I work for a core) is interested in haplotypes that occurr in the MHC gene in coyotes. Would you be willing to share your script or provide any additional insight? ...
written 8 days ago by gkuffel2230
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Comment: C: Getting Haplotypes from a VCF file
... Ummm, because any VCF file can be viewed as a csv or xls file. I provided this format to allow for easy viewing. If it would help anyone to have the actual VCF file I can easily provide that upon request. I wanted to know if I can get haplotypes from the data presented in the spreadsheet view of the ...
written 8 days ago by gkuffel2230
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Answer: A: freebayes haplotype calling (phased variants)
... Did you ever figure this out? I also am trying to get haploytpes from 450 bp amplicons. ...
written 9 days ago by gkuffel2230
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Getting Haplotypes from a VCF file
... Hi everyone, I am analying a data set for a user interested in looking at variants in the MHC gene of coyotes. I have used Freebayes to generate a VCF file. The user would now like haploytypes, does anyone know how to decipher that info from a file such as this vcf: https://docs.google.com/spreads ...
vcf haplotypes freebayes written 9 days ago by gkuffel2230 • updated 3 days ago by Ram13k
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Answer: A: Time Course Design in DESeq2
... Is it reasonable to use the design below to identify DEmiRNAs between patients?: ddsHTSeq1 <-DESeqDataSetFromHTSeqCount(sampleTable=sampleTable, directory=directory, design = ~ Time + Patient) ...
written 5 months ago by gkuffel2230
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Comment: C: Time Course Design in DESeq2
... I actually consider myself very well-versed with the DESeq2 manual and vignettes. Although there is a vignette that describes time course analysis using the Fission dataset I am having a difficult time relating it to my specific conditions. This is why I am reaching out to the community looking for ...
written 5 months ago by gkuffel2230
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Comment: C: Time Course Design in DESeq2
... Thanks for the reply. Both 1 & 2 can be accomplished in DESeq2. I am looking for a DESeq2 expert to help me set up the design and interaction terms. ...
written 5 months ago by gkuffel2230
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Time Course Design in DESeq2
... Hoping for some help. I can't seem to wrap my brain around how I should set up my design in DESeq2. Here are the details, I have 6 samples from each patients. I have two patients. Each sample represents a different timepoint of treatment. For each patient I have 2 age-matched healthy controls. So I ...
deseq2 timecourse mirna-seq written 5 months ago by gkuffel2230

Latest awards to gkuffel22

Popular Question 4 months ago, created a question with more than 1,000 views. For Variant Analysis on MiSeq Data
Popular Question 4 months ago, created a question with more than 1,000 views. For Mapping miRNA to the Human Genome with Bowtie2
Popular Question 5 months ago, created a question with more than 1,000 views. For Variant Analysis on MiSeq Data
Autobiographer 15 months ago, has more than 80 characters in the information field of the user's profile.

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