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Tool: MTMCSKAT package for GWAS with efficient resampling, parallelization
SKAT MTMC-SKAT
updated 15 months ago by 44k • written 15 months ago by ▴ 100
0
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0
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5.4k
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Comment: C: vcf2bed giving empty bed file as output
5.3 years ago by michael.nagle ▴ 100
1
vote
4
replies
5.4k
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vcf2bed giving empty bed file as output
GWAS genome genomics
updated 5.3 years ago by • 0 • written 7.0 years ago by ▴ 100
2
votes
9
replies
2.4k
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Post-GWAS: Determining whether SNPs represent an indel, given only SNPs
GWAS
updated 5.6 years ago by 20 • written 5.8 years ago by ▴ 100
0
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0
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1.3k
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Comment: C: Confounding factors when comparing effects of expression between RNA-seq samples
5.6 years ago by michael.nagle ▴ 100
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2
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1.3k
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Confounding factors when comparing effects of expression between RNA-seq samples and qPCR samples?
RNA-Seq qrtpcr qpcr transcriptomics expression
updated 5.7 years ago by 105k • written 5.7 years ago by ▴ 100
0
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0
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1.1k
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Job: REU / Research Experience for Undergraduate in genomic plant biology available at Oregon State University in Corvallis
Genomics Genetics Plant
updated 19 months ago by 44k • written 5.7 years ago by ▴ 100
0
votes
1
reply
2.7k
views
java.lang.NullPointerException error in IGVtools when trying to Find Motif
igvtools java
updated 5.8 years ago by 20 • written 8.5 years ago by ▴ 100
0
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2
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2.4k
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Comment: C: Post-GWAS: Determining whether SNPs represent an indel, given only SNPs
5.8 years ago by michael.nagle ▴ 100
0
votes
1
reply
2.4k
views
Comment: C: Post-GWAS: Determining whether SNPs represent an indel, given only SNPs
5.8 years ago by michael.nagle ▴ 100
0
votes
1
reply
2.4k
views
Comment: C: Post-GWAS: Determining whether SNPs represent an indel, given only SNPs
5.8 years ago by michael.nagle ▴ 100
0
votes
3
replies
1.7k
views
How to properly modify genome .gff and .fa to combine 2 loci that are really 1 gene
genomics
updated 6.6 years ago by 8.9k • written 8.0 years ago by ▴ 100
0
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0
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1.9k
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GWAS: Same workflow and inputs, different servers, very different output (EMMAX)
GWAS C EMMAX Server Cluster
6.6 years ago by michael.nagle ▴ 100
0
votes
5
replies
2.5k
views
Extra header column stopping EMMAX (C), but not seen in input files
emmax genomics Cpp plink GWAS
updated 17 months ago by • 0 • written 6.8 years ago by ▴ 100
0
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0
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2.5k
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Comment: C: Extra header column stopping EMMAX (C), but not seen in input files
6.8 years ago by michael.nagle ▴ 100
0
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1
reply
2.5k
views
Comment: C: Extra header column stopping EMMAX (C++), but not seen in input files
6.8 years ago by michael.nagle ▴ 100
0
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0
replies
3.5k
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Comment: C: "Unrecognized token: C" error when using emmax-kin to make kinship matrix for GW
6.8 years ago by michael.nagle ▴ 100
0
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1
reply
3.5k
views
Comment: C: "Unrecognized token: C" error when using emmax-kin to make kinship matrix for GW
6.8 years ago by michael.nagle ▴ 100
3
votes
4
replies
3.5k
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"Unrecognized token: C" error when using emmax-kin to make kinship matrix for GWAS
GWAS emmax kinship genomics
6.8 years ago by michael.nagle ▴ 100
0
votes
3
replies
3.5k
views
PLINK input files not found (adds .fam to input.bed)
gwas plink emmax genomics genome
updated 6.9 years ago by 20 • written 6.9 years ago by ▴ 100
0
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1
reply
3.5k
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Comment: C: PLINK input files not found (adds .fam to input.bed)
6.9 years ago by michael.nagle ▴ 100
0
votes
1
reply
1.4k
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Comment: C: Given QTLs and genome annotation, quickly list genes closest to QTLs
7.0 years ago by michael.nagle ▴ 100
0
votes
3
replies
1.4k
views
Given QTLs and genome annotation, quickly list genes closest to QTLs
GWAS genomics genome RNA-Seq
updated 7.0 years ago by ▴ 280 • written 7.0 years ago by ▴ 100
0
votes
1
reply
2.1k
views
GWAS: How to estimate probability of SNP association being result of one specific regulatory element, rather than others in LD
GWAS SNP LD Algorithms Calculus
updated 7.3 years ago by ★ 4.8k • written 7.3 years ago by ▴ 100
0
votes
0
replies
1.7k
views
Comment: C: How to properly modify genome .gff and .fa to combine 2 loci that are really 1 g
8.0 years ago by michael.nagle ▴ 100
1
vote
1
reply
1.9k
views
How to (1) combine two loci into one gene to correct genome and (2) re-run Cuffdiff to find correct FPKM of combined gene
genomics transcriptomics RNA-Seq RNA cDNA
8.2 years ago by michael.nagle ▴ 100
3
votes
1
reply
2.3k
views
Do multiple double peaks surely indicate both alleles of my PCR product are sequenced? (Sanger)
Sanger genomics sequencing
updated 8.2 years ago by 13k • written 8.2 years ago by ▴ 100
13
votes
3
replies
3.0k
views
In new genome, how is it decided which strand is forward/reverse?
genomics Assembly
updated 8.3 years ago by 3.1k • written 8.3 years ago by ▴ 100
0
votes
4
replies
3.1k
views
Trying to compare 3 versions of genome in IGV but can't sort in IGVtools or Samtools
genome igv samtools
updated 8.4 years ago by 20 • written 8.5 years ago by ▴ 100
0
votes
0
replies
1.4k
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Have .ab1 of 2 alleles in hybrid and .fa for 1, need .fa for the other
alleles sanger double peak trace
8.4 years ago by michael.nagle ▴ 100
0
votes
1
reply
1.7k
views
Upstream and downstream flanking sequences of adjacent genes do not appear to include each other on Phytozome, even though genes are adjacent?
genome
8.5 years ago by michael.nagle ▴ 100
1
vote
0
replies
1.6k
views
With SMART domain prediction, why is there no expectation value (E) for some domains?
domain smart expasy
8.5 years ago by michael.nagle ▴ 100
2
votes
2
replies
1.5k
views
Masking (NNN...) in published sequence caused by low read # or repetitiveness... how to know which?
genome masking
updated 8.5 years ago by 55k • written 8.5 years ago by ▴ 100
0
votes
0
replies
3.1k
views
Comment: C: Trying to compare 3 versions of genome in IGV but can't sort in IGVtools or Samt
8.5 years ago by michael.nagle ▴ 100
0
votes
0
replies
3.4k
views
Comment: C: How to BLAST 400 genes against genome at once?
8.5 years ago by michael.nagle ▴ 100
0
votes
1
reply
1.4k
views
Decimal in Accession number... .1 or .2 refers to latest annotation?
accession genome
updated 8.5 years ago by 148k • written 8.5 years ago by ▴ 100
1
vote
6
replies
3.4k
views
How to BLAST 400 genes against genome at once?
BLAST
updated 8.5 years ago by 7.6k • written 8.5 years ago by ▴ 100
1
vote
2
replies
1.9k
views
How to get sequence for a particular locus from .gff3 or .fa file?
genome
updated 8.5 years ago by ★ 9.6k • written 8.5 years ago by ▴ 100
0
votes
1
reply
3.1k
views
Comment: C: Trying to compare 3 versions of genome in IGV but can't sort in IGVtools or Samt
8.5 years ago by michael.nagle ▴ 100
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