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89 results • Page
1 of 2
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Views
Votes
Replies
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
6 days ago by
anna
▴ 20
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq
RNA-Seq
exon
updated 2 hours ago by
Sara
▴ 30 • written 6.7 years ago by
Lila M
★ 1.2k
3
votes
5
replies
267
views
Generating mpileup file using samtools
mpileup
samtools
updated 3 days ago by
Joe
21k • written 3 days ago by
Ruqaiya
• 0
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 3 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
3
votes
7
replies
348
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
6 days ago by
salias
• 0
2
votes
7
replies
427
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
updated 1 day ago by
Zhenyu Zhang
★ 1.2k • written 3 days ago by
Qroid
▴ 40
2
votes
3
replies
273
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 3 days ago by
dthorbur
★ 1.9k • written 3 days ago by
Vijith
▴ 30
2
votes
2
replies
208
views
Raw counts using stringtie
stringtie
RNA-seq
updated 3 days ago by
GenoMax
142k • written 3 days ago by
ahmad.sajad4541
• 0
2
votes
2
replies
1.8k
views
Parametric or non-parametric tests for qPCR significance testing between treatments?
qPCR
statistical test
parametric
non-parametric
updated 2 days ago by
e.r.zakiev
▴ 210 • written 3.8 years ago by
n.anuragsharma
▴ 40
2
votes
2
replies
2.6k
views
Pindel Segmentation Fault Error
pindel
updated 2 days ago by
Ruqaiya
• 0 • written 10.2 years ago by
Yuelin
▴ 20
2
votes
5
replies
931
views
Retrieval of Active site information programmatically
Catalytic
Python
Active
PDB
site
Site
updated 6 days ago by
Wayne
★ 2.0k • written 2.0 years ago by
arinjoy
• 0
1
vote
1
reply
232
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 5 days ago by
Ram
43k • written 6 days ago by
Jonathan Yoou
▴ 60
1
vote
8
replies
479
views
Downsampling fastq file
downsample
fastq
5 days ago by
marco.barr
▴ 90
1
vote
3
replies
262
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
23 hours ago by
Lada
▴ 30
1
vote
2
replies
290
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
5 days ago by
Nafi
• 0
1
vote
14
replies
2.4k
views
Extract gRNA sequence using cutadapt
cutadapt
trimming
crispr
sequencing
updated 3 days ago by
GenoMax
142k • written 4.5 years ago by
Swimming bird
▴ 20
1
vote
2
replies
228
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 6 days ago by
Ram
43k • written 6 days ago by
Ravita
• 0
1
vote
2
replies
225
views
Downloading full alignments from Pfam
pfam
1 day ago by
bef1
• 0
1
vote
3
replies
280
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 5 days ago by
GenoMax
142k • written 6 days ago by
jeffrey.maurer.informatics
• 0
1
vote
3
replies
235
views
Odd alignment question/finding
Alignment
updated 3 days ago by
barslmn
★ 2.1k • written 4 days ago by
poordumbsillyidiot
• 0
1
vote
6
replies
341
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 3 days ago by
GenoMax
142k • written 21 days ago by
eebloom
▴ 80
1
vote
2
replies
251
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
4 days ago by
rianna.collins
• 0
1
vote
0
replies
139
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
updated 8 hours ago by
zx8754
11k • written 2 days ago by
Emilie
▴ 10
1
vote
1
reply
138
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 4 days ago by
Ram
43k • written 4 days ago by
marco.barr
▴ 90
0
votes
1
reply
585
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 4 days ago by
mdav
• 0 • written 18 months ago by
Zoe
• 0
0
votes
0
replies
96
views
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
4 days ago by
James
▴ 10
0
votes
0
replies
96
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
4 days ago by
Vijith
▴ 30
0
votes
0
replies
100
views
Use of annotation of integrated Seurat object in single sample
Seurat
4 days ago by
Bine
▴ 60
0
votes
1
reply
225
views
Subsetting and merging back Seurat Object brings different results
Seurat
4 days ago by
Bine
▴ 60
0
votes
2
replies
190
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
3 days ago by
dtnondorf
• 0
0
votes
1
reply
148
views
Provean help
variant
Provean
updated 3 days ago by
Mensur Dlakic
★ 27k • written 4 days ago by
Arun Sai Kumar
• 0
0
votes
1
reply
543
views
HOMER on AWS
HOMER
updated 3 days ago by
clairechung112
• 0 • written 2.2 years ago by
Bogdan
★ 1.4k
0
votes
0
replies
144
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
3 days ago by
Jeyong
• 0
0
votes
0
replies
145
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
3 days ago by
rustykb
▴ 20
0
votes
0
replies
246
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
3 days ago by
NorbertK
• 0
0
votes
0
replies
127
views
Modify plot R mtDNA indel
plot
mtDNA
R
3 days ago by
marco.barr
▴ 90
0
votes
0
replies
129
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic
Variant
predisposition
3 days ago by
mikemakaveli1
• 0
0
votes
0
replies
135
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
3 days ago by
Javier
• 0
0
votes
6
replies
389
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 2 days ago by
swbarnes2
14k • written 3 days ago by
Erina
• 0
0
votes
0
replies
132
views
Empty table plot using plotGseaTable()
FGSEA
2 days ago by
Chris
▴ 260
0
votes
1
reply
186
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 2 days ago by
GenoMax
142k • written 2 days ago by
Ximena
• 0
0
votes
1
reply
159
views
HCL database download
database
HCL
human
updated 2 days ago by
GenoMax
142k • written 2 days ago by
sooni
▴ 20
0
votes
2
replies
238
views
Downloading older version of a tool
Alignment
tools
2 days ago by
Ruqaiya
• 0
0
votes
1
reply
180
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 2 days ago by
Ram
43k • written 2 days ago by
Valentina
• 0
0
votes
1
reply
225
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 2 days ago by
Thanujay S
• 0 • written 3 days ago by
yahn
• 0
0
votes
0
replies
118
views
Homer motif analysis
Homer
2 days ago by
daffodil
▴ 10
0
votes
0
replies
97
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
1 day ago by
Yoosef
▴ 60
0
votes
0
replies
89
views
Seurat V5 integration
Seurat
samples
integration
combine
1 day ago by
starswillfade
▴ 10
0
votes
0
replies
87
views
Clarification on StringTie's `--merge` parameters
stringtie
stringtie-merge
1 day ago by
DGTool
• 0
0
votes
0
replies
80
views
Looking for phytopathogenic, Nitrogen-Fixing, and Growth-Promoting databases for Metagenomic Analysis
Bacteria
Metagenomics
Database
1 day ago by
Christopher
• 0
89 results • Page
1 of 2
Recent Votes
Comment: High Malat-1 expression in single cell data
A: Meme-Tools: Bit score
Meme-Tools: Bit score
Meme-Tools: Bit score
Comment: error in R code
DEXSeq multiple time points
How to find the most frequent alternative-splicing event from DEXSEQ data?
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Answer: error in R code
by
Matthias Zepper
4.6k
I quickly googled [the source code of that function][1], and the error is triggered by this condition: if(length(wn) < 1 || !is.whol…
Comment: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
by
kalavattam
▴ 190
Thanks for the explanation. I noticed and corrected a typo in which "*read* reverse strand" initially read as "*mate* reverse strand" in t…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
sovrappensiero
▴ 90
It's a commercial product, a *Staphylococcus hominis* genome. This species is not found in the DADA2 results, so I guess DADA2 is not ident…
Comment: Question regarding WGCNA
by
Ram
43k
Plots are incomplete without legends. Please share the complete plot with mappings for shape and color.
Comment: Quetion regarding WGCNA
by
deepak
• 0
Thank you for your reply andres.firrincieli. I have attached the PCA plot of the expression data used in the WGCNA. ![enter imag…
Comment: Design matrix Differential expression analysis
by
SHN
▴ 40
Got it, thank you for your response. SN
Comment: How to interpret DEXseq results in therms of significance
by
Sara
▴ 30
Hi, I used write.table(as.data.frame(DEXSeqResults(MyObj)), "Results.tsv", quote=FALSE, sep="\t", dec=".") to save the result but I recei…
Comment: Tissue-specific DEG analysis with DEseq2
by
M.
▴ 30
Can I ask what do you exactly mean by same experiment? If you are talking about the same donor and the same procedure, unfortunately, not a…
Comment: install package: package ‘gmwm’ is not available for this version of R
by
Ram
43k
Find someone with computer skills near you and consult them. From your posts on the forum, it's clear that you need help at a level that we…
Comment: Gene Specific coverage from WGS data
by
GenoMax
142k
This is not going to work no matter what program you use since the chromosome identifiers in your GTF (`MN908947.3 `) do not match your BA…
Comment: install.packages("imudata") - package ‘imudata’ is not available for this versio
by
Ram
43k
Read the answers in the post, understand them and try to implement them.
Comment: High Malat-1 expression in single cell data
by
t.montserrat.ayuso
▴ 10
Just using the normalized expression of Malat1 works.
Comment: Can I merge Hi-C fastq files from different lanes?
by
Winter
• 0
Awesome, thank you for the concise and straight-forward answer!
Comment: error in R code
by
ATpoint
82k
Look, before you keep posting these sorts of questions and might gross of users, please read and follow https://www.biostars.org/p/357878/ …
Comment: Gene Specific coverage from WGS data
by
1769mkc
★ 1.2k
"Also if is there any other quick way to find gene specific coverage" can you give some example so that its bit more clear what do you mean…
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