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50 results • Page
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Showing top results for tag:
plink
•
reset
0
votes
0
replies
30
views
Merging bfiles
merge
fam
plink
bfile
bed
3 hours ago by
aj123
▴ 120
0
votes
0
replies
130
views
Pedigree information
pedigree
plink
king
2 days ago by
heureuse
• 0
0
votes
0
replies
134
views
How to calculate inbreeding coefficient out of ROH (Plink)
plink
7 days ago by
t-ishige
• 0
0
votes
1
reply
245
views
Plink HWE QC question
HWE
Plink
p-value
updated 10 days ago by
bk11
★ 2.9k • written 10 days ago by
janny.lau
▴ 10
3
votes
3
replies
405
views
Ancestry estimation using 1000 genomes as reference
ancestry
plink
1000genomes
updated 26 days ago by
Jeremy Leipzig
22k • written 28 days ago by
kasgel
• 0
0
votes
1
reply
280
views
Updating phenotype column for .ped .fam files (PLINK --pheno not working)
phenotype
PLINK
--pheno
GWAS
binary
updated 4 weeks ago by
bk11
★ 2.9k • written 4 weeks ago by
sabrilo171
▴ 10
4
votes
5
replies
544
views
LD Pruning in GWAS
PLINK
PCA
pruning
LD
GWAS
updated 4 weeks ago by
LauferVA
4.4k • written 4 weeks ago by
Smriti
▴ 30
1
vote
1
reply
392
views
How to deal with warnings from PLINK while performing QC using HAPMAP data ?
QC
Hapmap
PLINK
GWAS
updated 4 weeks ago by
Kevin Blighe
88k • written 6 weeks ago by
Yugan Gogul Muthukumar
• 0
0
votes
2
replies
817
views
Apply Plink2 Score - Error Invalid chromosome code
plink
plink2
pgsc_calc
plink2score
updated 5 weeks ago by
Ruijiang HAN
▴ 10 • written 14 months ago by
h171linux
• 0
0
votes
4
replies
505
views
PLINK error doing a GWAS
phenotype
PLINK
covariates
association
GWAS
updated 5 weeks ago by
chrchang523
11k • written 5 weeks ago by
david.badenas.01
• 0
1
vote
6
replies
552
views
Analyzing PCA Clustering from PLINK Output
plink
4 weeks ago by
Smriti
▴ 30
0
votes
0
replies
149
views
Generate the snpfile.txt (for BLUPF90 input) in 0125 format from plink flat file (.map and .ped)?
Genotype
BLUPF90
PLINK
updated 5 weeks ago by
GenoMax
145k • written 5 weeks ago by
tvibhaps
▴ 10
0
votes
5
replies
603
views
Segmentation fault PLINK 1.90b
PLINK
updated 5 weeks ago by
chrchang523
11k • written 7 weeks ago by
Alexandros.Frydas
▴ 30
0
votes
0
replies
168
views
BCftools call when using -v -V indels vs using -V indels only
BCftools
plink
6 weeks ago by
Jimmy M
• 0
1
vote
1
reply
285
views
Can i use population as a trait to perform GWAS?
Hapmap
PLINK
GWAS
QC
updated 6 weeks ago by
dthorbur
★ 2.4k • written 6 weeks ago by
Yugan Gogul Muthukumar
• 0
1
vote
2
replies
301
views
How to fix this error while performing QC in PLINK "Warning: 228 het. haploid genotypes present"
Hapmap
PLINK
GWAS
QC
6 weeks ago by
Yugan Gogul Muthukumar
• 0
0
votes
0
replies
216
views
Convert Illumina Final Report.txt file into PLINK input files (.fam, .lgen, .ped etc)
PLINK
7 weeks ago by
Alexandros.Frydas
▴ 30
0
votes
1
reply
257
views
PCA Genotyping rate 1000genome and own data
quality
genotypingrate
pca
plink
genomics
updated 8 weeks ago by
LChart
4.3k • written 8 weeks ago by
curious_butterfly
• 0
0
votes
0
replies
194
views
Does Plink under perform ? ( GWAS )
snp
gwas
qq-plot
plink
updated 8 weeks ago by
GenoMax
145k • written 8 weeks ago by
basnet.soren
• 0
0
votes
1
reply
298
views
Multi allelic variants extraction with plink
plink
multiallelic-variants
updated 8 weeks ago by
chrchang523
11k • written 8 weeks ago by
_quantum_girl_
▴ 40
5
votes
12
replies
4.4k
views
10 follow
ADMIXTURE Segmentatio fault
admixture
plink
vcf
updated 9 weeks ago by
Etienne DVRK
• 0 • written 3.3 years ago by
pmc.sa
▴ 40
0
votes
0
replies
226
views
How to best check allele flipping between bed files?
plink
bed
10 weeks ago by
DN99
▴ 20
3
votes
3
replies
559
views
LD SNP pruning with plink
LD-pruning
plink
10 weeks ago by
celia
▴ 10
0
votes
0
replies
227
views
mismatch allele problem PLINK
PLINK
updated 10 weeks ago by
Ram
44k • written 11 weeks ago by
luca.sclisizzo
• 0
1
vote
1
reply
266
views
Discrepancies in F Coefficient and Heterozygosity Estimates
population-genetics
F-coefficient
plink
vcftools
updated 11 weeks ago by
Ram
44k • written 11 weeks ago by
eleftosi
• 0
3
votes
5
replies
696
views
ROH and Manhattan plot
ROH
Manhattan
plink
updated 3 months ago by
bk11
★ 2.9k • written 3 months ago by
Star:)
▴ 50
0
votes
8
replies
1.0k
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
genomics
plink
updated 3 months ago by
Ram
44k • written 4 months ago by
ajbarrett98
• 0
0
votes
0
replies
297
views
I need to binary plink files of human genome reference build37, however, Im completely lost and have no idea from where to begin
bplinkfiles
human
genome
plink
updated 3 months ago by
GenoMax
145k • written 3 months ago by
Marcos
• 0
1
vote
2
replies
424
views
Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLINK's logistic regression analysis and covariates
PLINK
GWAS
SNP
4 months ago by
F110152169
• 0
1
vote
2
replies
870
views
Checking chromosome builds for genotyping data
GWAS
Liftover
PLINK
updated 4 months ago by
Muhammad
• 0 • written 2.9 years ago by
mari.lynne
• 0
1
vote
5
replies
586
views
Annotating file using bcftools
annotation
plink
bcftools
4 months ago by
kl
▴ 10
0
votes
1
reply
330
views
Generating .bed file and .map file for polyploid vcf file through plink
bed
polyploid
map
plink
updated 4 months ago by
chrchang523
11k • written 4 months ago by
analyst
▴ 50
0
votes
0
replies
241
views
Trouble converting tfam and tped to map and ped files
plink
ped
tfam
tped
map
4 months ago by
Samantha
• 0
0
votes
0
replies
196
views
Summary Statistics SNPs not found in Target data
SNP
plink
PRS
updated 4 months ago by
Ram
44k • written 4 months ago by
curious_butterfly
• 0
4
votes
1
reply
391
views
LD-prune variants while maintaining a list of SNPs
snp
vcf
plink
filtering
independent
updated 4 months ago by
zx8754
12k • written 4 months ago by
Jautis
▴ 580
0
votes
5
replies
682
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 4 months ago by
chrchang523
11k • written 4 months ago by
curious
▴ 800
1
vote
0
replies
255
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
updated 4 months ago by
zx8754
12k • written 4 months ago by
Emilie
▴ 10
8
votes
16
replies
1.8k
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 5 months ago by
bk11
★ 2.9k • written 6 months ago by
Sofia
• 0
1
vote
3
replies
2.7k
views
Problem to remove subset of patients with plink
plink
PED
updated 5 months ago by
chrchang523
11k • written 6.6 years ago by
Ginevra
▴ 10
1
vote
1
reply
584
views
Plink merge errors.
cygwin64
bed
PLINK
5 months ago by
Dinmukhamed
• 0
0
votes
0
replies
289
views
Conversion to tree format
PLINK
bed
Figtree
SplitsTree
updated 5 months ago by
Ram
44k • written 5 months ago by
Dinmukhamed
• 0
0
votes
0
replies
318
views
Pruning with plink finds a majority of SNPs in very high LD
LD
SNP
plink
pruning
5 months ago by
enferdeflame
• 0
0
votes
0
replies
262
views
Struggling to lift genome builds
PLINK
liftover
GWAS
updated 5 months ago by
GenoMax
145k • written 5 months ago by
srimmer
• 0
0
votes
2
replies
460
views
Merging Outputs from plink --assoc and --hardy to Produce Table
PLINK
PANDAS
R
5 months ago by
Koketso
• 0
4
votes
4
replies
996
views
How do I install plink2 on a mac?
plink2
plink
updated 5 months ago by
zx8754
12k • written 5 months ago by
emilija.romic
▴ 10
0
votes
2
replies
387
views
Can't figure out plink --sample-diff
plink
5 months ago by
curious
▴ 800
2
votes
4
replies
1.6k
views
PLINK p value returning NA
GWAS
PLINK
updated 5 months ago by
chrchang523
11k • written 24 months ago by
Sin Yu, Lin
• 0
1
vote
1
reply
592
views
PLINK multivariable GLM output: p-value without BETA and SE
linear-model
glm
plink
updated 5 months ago by
chrchang523
11k • written 5 months ago by
dsbusiness135
▴ 10
2
votes
1
reply
1.1k
views
Merging multiple PLINK files
plink
merging
updated 6 months ago by
Dinmukhamed
• 0 • written 16 months ago by
Nejla
▴ 20
0
votes
0
replies
263
views
details about PCA in plink 2.0: eigenvectors, PCs, scores
gwas
plink
pca
6 months ago by
kaybelter
• 0
50 results • Page
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Recent Votes
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Comment: Numreads from samtools for Differential Expression
Answer: How to compile Multiz
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Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
GenoMax
145k
Can you check using `featureCounts` to make sure things look reasonable with alignments? You could also use `salmon` to do transcript quant…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
GenoMax
145k
Since we don't have access to your data we can't comment. Check the integrity of your input data files. Validate the files if you are not s…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
GenoMax
145k
https://www.biostars.org/u/145859/ : Use `ADD REPLY/ADD COMMENT` to add additional information to existing threads. `ADD YOUR ANSWER` is me…
Comment: How to compile Multiz
by
GenoMax
145k
Please do not ask questions unrelated to the original post in this thread. Post a new question.
Comment: How to compile Multiz
by
Santex
• 0
I could install multiz from it! Thank you very much. Please help me out with the problem below. I run multiz like below. (myenv) tak…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Pallondyle
• 0
One of them looks okay, but I don't quite believe it. ```R > table(df$`intermediate_data.OE1_1_.genes.results`==0) FALSE TRUE 21200 2…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Pallondyle
• 0
It seems that the files that generated the results also have significant issues. Except for one sample, all other samples only have over 20…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Pallondyle
• 0
Their .fq files all look similar, should I rerun these programs?
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
GenoMax
145k
> Cannot open intermediate_data/OE_NC_2_.temp/OE_NC_2__alignable_1.fq! It may not exist. Looks like you are missing some files. BTW this …
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Pallondyle
• 0
The most torturous thing is that some groups did indeed generate results. ``` ls intermediate_data KO1_1_.stat KO1_3_.isoforms…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Pallondyle
• 0
However, OE1_2 and OE1_3 are not the only groups experiencing problems. I tried another non-empty file, and: ``` rsem-calculate-expression …
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
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oops ``` file *.out.bam KO1_2Aligned.sortedByCoord.out.bam: gzip compressed data, extra field KO1_2Aligned.toTranscriptome.out.bam: …
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read https://github.com/samtools/samtools/blob/develop/sam_view.c * allocate a new bam1_t* b = bam_init1 * open the input file: sam_op…
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164k
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by
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Thank you, it worked almost after two months of struggle, I nearly deleted everything and reinstalled it, I assume the problem was someth…
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