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184 results • Page
3 of 4
Sort: Votes
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0
votes
1
reply
223
views
How to convert Haps file to vcf file?
pre-phasing
GWAS
imputation
updated 6 days ago by
curious
▴ 750 • written 7 days ago by
SeoGyun
• 0
0
votes
2
replies
228
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 6 days ago by
Ram
43k • written 7 days ago by
sainavyav22
• 0
0
votes
1
reply
203
views
extract viral protein of interest from 10k whole viral genomes
nBLAST
viral-genome
updated 6 days ago by
Ram
43k • written 6 days ago by
Shwetha
• 0
0
votes
0
replies
164
views
Marker Features variance by cluster, sample, and treatment group
Seurat
scATAC-seq
ArchR
updated 6 days ago by
Ram
43k • written 6 days ago by
naomiboldon
• 0
0
votes
4
replies
300
views
Correlation Analysis
statistics
methylation
NGS
expression
6 days ago by
Researcher
▴ 30
0
votes
2
replies
293
views
How are score_weights calculated in this code?
single-cell
5 days ago by
carolofharvest
▴ 40
0
votes
1
reply
230
views
input file in rmats
rmats
updated 5 days ago by
Mathew
▴ 140 • written 7 days ago by
Lambodarswain316
• 0
0
votes
0
replies
128
views
News:
Online course: An Introduction to Nanopore Direct RNA Sequencing
Nanopore
RNAseq
5 days ago by
carlopecoraro2
★ 2.5k
0
votes
11
replies
533
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
4 days ago by
Tuck898
• 0
0
votes
1
reply
242
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA
RNA-seq
Nomalization
Microarray
updated 4 days ago by
Zhenyu Zhang
★ 1.2k • written 7 days ago by
jain72744
▴ 10
0
votes
2
replies
230
views
Obtaining Infinium Methylation450K manifest for hg38
TCGA
hg38
methylation
Illumina
updated 4 days ago by
Zhenyu Zhang
★ 1.2k • written 8 days ago by
elisheva
▴ 120
0
votes
2
replies
295
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 4 days ago by
Zhenyu Zhang
★ 1.2k • written 13 days ago by
yahn
• 0
0
votes
5
replies
330
views
How to convert normalized BigWig file to count matrix?
count-matrix
BigWig
4 days ago by
feather-W
• 0
0
votes
0
replies
109
views
lncRNA
tcga
lncrna
4 days ago by
jain72744
▴ 10
0
votes
1
reply
194
views
Generating .bed file and .map file for polyploid vcf file through plink
bed
polyploid
map
plink
updated 4 days ago by
chrchang523
10k • written 9 days ago by
analyst
▴ 50
0
votes
2
replies
229
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
4 days ago by
analyst
▴ 50
0
votes
4
replies
396
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
4 days ago by
beginner123
• 0
0
votes
7
replies
426
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 4 days ago by
Mohamed Abderrahmane
▴ 20 • written 17 days ago by
matteo.levorato
• 0
0
votes
1
reply
157
views
Manual Assembly and Protein Translation, HELP, assignment revision
sequence
university
assembly
protein
genomics
updated 4 days ago by
Philipp Bayer
8.5k • written 4 days ago by
samRayne
• 0
0
votes
2
replies
209
views
Output file of samtools flagstat empty
samtools-flagstat
updated 4 days ago by
colindaven
6.4k • written 4 days ago by
ramendra.sarma
• 0
0
votes
0
replies
101
views
Reference panel of normals for ensembl named refgenome
Mutect2
3 days ago by
gernophil
▴ 80
0
votes
1
reply
530
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
updated 3 days ago by
aw7
▴ 300 • written 27 days ago by
abhishekghadge
• 0
0
votes
0
replies
88
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
3 days ago by
JACKY
▴ 140
0
votes
5
replies
316
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
3 days ago by
SilhouetteQ
• 0
0
votes
1
reply
153
views
Mouse ribosome sequences in fasta format
fasta
mm10
rRNA
updated 3 days ago by
GenoMax
142k • written 4 days ago by
octpus616
▴ 100
0
votes
0
replies
103
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
3 days ago by
atariw
▴ 10
0
votes
1
reply
161
views
consensus sequence calling
consensus
updated 3 days ago by
bk11
★ 2.4k • written 3 days ago by
Ghada
• 0
0
votes
0
replies
104
views
reference-free assembly error assessment tools
assembly
3 days ago by
lagartija
▴ 160
0
votes
3
replies
352
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
3 days ago by
mropri
▴ 150
0
votes
2
replies
423
views
News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
3 days ago by
David Langenberger
11k
0
votes
1
reply
149
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 3 days ago by
Ram
43k • written 3 days ago by
eking28
• 0
0
votes
1
reply
142
views
Splitting Seurat object by sample layers
seurat
updated 3 days ago by
Ram
43k • written 3 days ago by
kilcdincer
▴ 10
0
votes
3
replies
190
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat
single-cell
scRNA-seq
R
updated 3 days ago by
Ram
43k • written 3 days ago by
yau
• 0
0
votes
6
replies
419
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
genomics
plink
updated 3 days ago by
Ram
43k • written 6 days ago by
ajbarrett98
• 0
0
votes
0
replies
118
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass-spectrometry
Proteins
updated 3 days ago by
Ram
43k • written 18 days ago by
atharvakarkare14
▴ 40
0
votes
1
reply
146
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Cancer-Research
ATAC-seq
updated 3 days ago by
Ram
43k • written 10 days ago by
David
• 0
0
votes
1
reply
245
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Mendelian-Randomization
updated 3 days ago by
Ram
43k • written 7 days ago by
Nikki
• 0
0
votes
1
reply
160
views
How to process Bulk WES data?
WES
WGS
updated 3 days ago by
GenoMax
142k • written 3 days ago by
wyuan37
• 0
0
votes
4
replies
3.6k
views
SNPEff database building error
SNP
updated 3 days ago by
Fungal genetics
• 0 • written 7.1 years ago by
ntyagi654
• 0
0
votes
1
reply
160
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 3 days ago by
GenoMax
142k • written 3 days ago by
cedric.blais
• 0
0
votes
0
replies
181
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
deeptools
correlation
3 days ago by
Emily
▴ 20
0
votes
3
replies
342
views
Snakemake wrapper issue
fastqc
snakemake
updated 3 days ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
0
votes
0
replies
93
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
3 days ago by
Spring
• 0
0
votes
2
replies
175
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
3 days ago by
IdaHao0921
• 0
0
votes
4
replies
257
views
Galaxy StringTie error
stringtie
galaxy
2 days ago by
trkfs
• 0
0
votes
3
replies
200
views
How to access GWAVA software of data
GWAVA
updated 2 days ago by
GenoMax
142k • written 2 days ago by
nonaddldy
▴ 10
0
votes
3
replies
210
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 2 days ago by
GenoMax
142k • written 3 days ago by
RNAseqer
▴ 270
0
votes
0
replies
109
views
Is there a real ground truth for CNV data?
CNV
2 days ago by
jennyp0706
• 0
0
votes
1
reply
143
views
Post-imputation QC for input into GWAS analyses
gwas
prs
updated 2 days ago by
LauferVA
4.2k • written 2 days ago by
graeme.thorn
▴ 100
0
votes
3
replies
254
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 2 days ago by
noodle
▴ 580 • written 2 days ago by
doramora
▴ 10
184 results • Page
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Answer: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Having duplicate gene symbols is pretty common. Why do you need to work with gene symbols? To compare them to external datasets? Or just fo…
Comment: Merge clusters in Seurat UMAP
by
kilcdincer
▴ 10
It did not help either. But I got the answer [here][1] Thank you! [1]: https://github.com/satijalab/seurat/issues/8902
Comment: How to generate table_annovar from VCF input?
by
Pierre Lindenbaum
161k
there is no `--allsample` option in the "usage" screen you're showing. I suspect you're using an old version ?
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
egascon
• 0
Thank you very much again. I have learned a lot of things.
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
egascon
• 0
It's a microarryay experiment, not RNASeq
Comment: Sam file Header problem
by
Pierre Lindenbaum
161k
https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups
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by
DGTool
▴ 20
I have also recently come across another global alignment algorithm that was recently released which could seem pretty interesting to test …
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
b.contreras.moreira
▴ 190
Not sure, you might ask in the repo, please share here the response if you find it
Comment: How to generate table_annovar from VCF input?
by
LucisTheFather
• 0
Would you be more specific to your question? Do you mean how to debug this syntax error?
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hophuquy0944
• 0
thank you
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Tony
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I think this method should be applicable to all high-throughput single-cell RNA-seq platforms. Although the method of determining cell spec…
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The dataset you want (taestivum_eg_gene) exists within the "plants_mart" schema, not the default schema. Your current code assumes the defa…
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Nyksubuz
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You could use [this][1] [1]: https://ggplot2.tidyverse.org/reference/geom_segment.html
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It might be because the gene symbol is not found in the KEGG database. Add some extra error handling before parsing the results or do a man…
Comment: Sam file Header problem
by
saifulislam99121
• 0
Thank you for your reply. I am not very much sure about this RG. Can you explain me a bit?
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