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122,199 results • Page
646 of 2444
Sort: Rank
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Votes
Replies
5
votes
9
replies
2.0k
views
How can I extract mostly expressed genes from a series matrix?
WGCNA
R
RNA-seq
4.5 years ago by
microorganism_001
▴ 30
1
vote
3
replies
1.4k
views
Downloading data from 1000Genomes
1000Genomes
vcf
updated 4.5 years ago by
zx8754
12k • written 4.5 years ago by
peter
▴ 20
0
votes
4
replies
1.7k
views
> 90% samples, DP > 10
VCF
R
DP
updated 4.5 years ago by
sbstevenlee
▴ 480 • written 4.5 years ago by
Filago
▴ 110
6
votes
4
replies
2.9k
views
Genome annotation file GFF3 and GTF same? interchangeable?
GTF
GFF3
NGS
ANNOTATION
4.5 years ago by
SKY
▴ 60
0
votes
3
replies
1.1k
views
Forum:
what for masters?
microbio
masters
updated 4.5 years ago by
Dunois
★ 2.9k • written 4.5 years ago by
barn.nishtha
• 0
0
votes
1
reply
865
views
PCA and bar plot in Tripal
tripal
plots
updated 4.5 years ago by
zx8754
12k • written 4.5 years ago by
felipead66
▴ 120
0
votes
2
replies
1.1k
views
How to convert RNAhybrid output to data frame
RNAhybrid
updated 4.5 years ago by
Michael
56k • written 4.5 years ago by
Wakala
• 0
2
votes
2
replies
1.7k
views
Using DAVID Web Service to classify genes into functional groups
DAVID-Web-Service
david
4.5 years ago by
langziv
▴ 70
0
votes
0
replies
1.0k
views
GATK MUTECT2
gatk
mutect2
updated 2.7 years ago by
Ram
45k • written 4.5 years ago by
Hyeong Seok
• 0
0
votes
1
reply
638
views
how to removed the nucleotides from a fastq file (single-end) in conditional
PAS-seq
updated 4.5 years ago by
Dunois
★ 2.9k • written 4.5 years ago by
17318598206
▴ 30
0
votes
3
replies
1.9k
views
Mapping fastq files to reference genome
reference-genome
mapping
fastq
updated 2.2 years ago by
Ram
45k • written 4.5 years ago by
A_heath
▴ 180
1
vote
4
replies
1.4k
views
Header conflicts in concatenated FASTQ file?
FASTQ
RNA-seq
concatenate
4.5 years ago by
Dunois
★ 2.9k
0
votes
1
reply
905
views
samtools depth vs Rsamtools pileup
Samtools
RSamtools
Bioconductor
R
4.5 years ago by
chasem
▴ 50
6
votes
4
replies
2.6k
views
how to removed the first two nucleotides from a fastq file (single-end)
CGAE-seq
fastq
updated 4.5 years ago by
cpad0112
21k • written 4.5 years ago by
17318598206
▴ 30
0
votes
0
replies
841
views
Truncated sam File from Resfinder Database in MGmapper
mapping
4.5 years ago by
hafiz.talhamalik
▴ 350
0
votes
1
reply
1.0k
views
Query regarding WGCNA module formation
WGCNA
RNA-seq
updated 4.5 years ago by
i.sudbery
22k • written 4.5 years ago by
microorganism_001
▴ 30
0
votes
3
replies
1.0k
views
function annotation
GO
updated 4.5 years ago by
Dunois
★ 2.9k • written 4.5 years ago by
chinu
• 0
0
votes
0
replies
641
views
how to annotate mapping peaks within a defined genomic region?
piRNA
genome
RNA-seq
annotation
4.5 years ago by
tianshenbio
▴ 190
1
vote
2
replies
2.2k
views
How to print the header of bed file and the lines that belong to chromosome 2
fastq
Bed_files
fasta
Bash
updated 4.4 years ago by
Ram
45k • written 4.5 years ago by
FadyNabil
▴ 20
0
votes
1
reply
843
views
Best graph/plot to convey gene expression differences across time?
graph
plot
Gene
Expression
R
updated 4.5 years ago by
Nitin Narwade
★ 1.7k • written 4.5 years ago by
Qamarul
• 0
3
votes
5
replies
2.0k
views
How to use lapply to extract taxonomic information in my species list?
R
4.5 years ago by
DNAngel
▴ 260
0
votes
2
replies
1.3k
views
Forum:
Study Materials
learning
study
materials
4.5 years ago by
AHa
• 0
1
vote
2
replies
1.3k
views
Duplicate markers
duplicate
plink
markers
4.3 years ago by
Alexandra
▴ 20
0
votes
3
replies
1.6k
views
SOAPaligner- 2bwt-builder segmentation fault
soapaligner
c
linux
updated 4.4 years ago by
Ram
45k • written 4.5 years ago by
lafced
• 0
0
votes
3
replies
2.0k
views
How to perform GO enrichment for non-model species
non-model-species
Gene-Ontology
GO-enrichment
4.4 years ago by
Kumar
▴ 170
0
votes
0
replies
1.3k
views
What is the file .mums created by mummer ?
Mummer
Alignment
Mummerplot
Genome
updated 4.4 years ago by
Ram
45k • written 4.5 years ago by
Student
▴ 30
1
vote
0
replies
948
views
Discussion on binning multiple metagenomes at the same time?
binning
metagenomics
mags
4.5 years ago by
O.rka
▴ 750
6
votes
9
replies
3.6k
views
Preparing Target Data
PGS
PRS
PRSice
updated 4.5 years ago by
Sam
★ 4.8k • written 4.5 years ago by
Jenish
▴ 20
1
vote
6
replies
2.0k
views
Anyone can help me to interpret this ClonalFrameML output?
Recombination
ClonalFrameML
Phylogenies
updated 3.8 years ago by
Joe
22k • written 4.5 years ago by
chantalrenauminguez
• 0
0
votes
2
replies
962
views
How to get domain/kingdom name in a table of taxid in R tidyverse?
R
4.5 years ago by
DNAngel
▴ 260
2
votes
4
replies
1.7k
views
Rsamtools: get nucleotide of read ID X at position P
rsamtools
4.5 years ago by
francois
▴ 90
1
vote
2
replies
1.3k
views
Get by-strand base counts at position from cram file
igv
cram
count
strand
details
4.5 years ago by
davenomiddlenamecurtis
▴ 20
3
votes
5
replies
1.2k
views
Developing algorithms
Microbial
genomics
updated 4.5 years ago by
Joe
22k • written 4.5 years ago by
jenny_govind
• 0
1
vote
1
reply
1.1k
views
How to access specific gene data from the NCBI Gene database with Biopython
Biopython
updated 4.5 years ago by
Istvan Albert
103k • written 4.5 years ago by
João Afonso
• 0
4
votes
3
replies
6.0k
views
kraken2 unclassified output does not work with paired reads?
Kraken2
updated 4.5 years ago by
Istvan Albert
103k • written 4.5 years ago by
DNAngel
▴ 260
4
votes
3
replies
1.5k
views
What do the samtools column names mean
NGS
samtools
updated 4.5 years ago by
Ram
45k • written 4.5 years ago by
Ishak
• 0
0
votes
6
replies
2.5k
views
How to identify snps in gene
snp
identification
4.5 years ago by
Ak
▴ 60
1
vote
1
reply
764
views
Extract co-ordinate for iCLIP data?
sequencing
linux
RNA
updated 4.5 years ago by
Istvan Albert
103k • written 4.5 years ago by
PK
▴ 130
2
votes
1
reply
1.9k
views
Preparing data for kinship calculations
PRUNING
VCF
PLINK2
KING
updated 4.5 years ago by
Ram
45k • written 4.5 years ago by
Filago
▴ 110
2
votes
3
replies
1.3k
views
plotting stacked bar plot with different number and kinds of variables
stackedbarplot
ggplot
4.5 years ago by
Curls
▴ 40
1
vote
6
replies
3.4k
views
how to implement a database with several FASTA files
Database
NCBI
FASTA
updated 4.5 years ago by
Istvan Albert
103k • written 4.5 years ago by
Debut
▴ 20
1
vote
3
replies
2.7k
views
PAM250 and BLOSUM62 probability of substitution matrices
blosum
matrix
pam
updated 4.5 years ago by
Mensur Dlakic
★ 30k • written 4.5 years ago by
Maria Saeed
• 0
0
votes
0
replies
789
views
Goseq - Pwf: Error In If (Hi <= Low) { : Missing Value Where True/False Needed
r
goseq
ontology
Gene
GO
updated 4.5 years ago by
Ram
45k • written 4.5 years ago by
ryme
▴ 30
0
votes
0
replies
698
views
How to derive an inverse simpson index(alpha diversity) from the phylosift results
phylosift
alpha
diversity
4.5 years ago by
tmfdk0819
• 0
0
votes
2
replies
1.2k
views
Clustering artefacts when processing single-nucleus RNAseq
single-cell
RNA
Seurat
UMAP
4.5 years ago by
MikeV
▴ 10
4
votes
8
replies
9.3k
views
Help with designing limma contrast matrix
limma
software error
updated 2.7 years ago by
Kevin Blighe
★ 90k • written 7.7 years ago by
zizigolu
★ 4.4k
1
vote
4
replies
2.9k
views
deeptools 3.5 plotCorrelation
ChIP-Seq
sequencing
plotCorrelation
next-gen
deeptools
updated 4.5 years ago by
Carlo Yague
9.0k • written 4.5 years ago by
jjp55
▴ 20
4
votes
11
replies
11k
views
7 follow
Single cell DEG analysis. Wildly different results from different FindMarkers test
rna-seq
seurat
updated 4.5 years ago by
Ram
45k • written 5.3 years ago by
jevanveen
▴ 20
0
votes
5
replies
2.2k
views
TCGA data Query (GDCquery): external_gene_name " are missing
TCGABiolinks
R
TCGA
updated 2.7 years ago by
Ram
45k • written 4.5 years ago by
H. Z. Amini
• 0
7
votes
1
reply
1.5k
views
Herald:
The Biostar Herald for Wednesday, June 02, 2021
herald
updated 4.5 years ago by
Istvan Albert
103k • written 4.5 years ago by
Biostar
3.7k
122,199 results • Page
646 of 2444
Recent Votes
Answer: Midpoint rooting IQTREE newick file moves node support around
Answer: Subsetting before QC in Spatial Transcriptomics
Answer: Feature Counts vs Salmon quantification
Comment: Feature Counts vs Salmon quantification
Answer: Can i use orthofinder for small protein datasets and not full proteome?
Comment: Comparison of different RNAseq data sets
Comment: ID unifiying across different datasets
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Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Arup Ghosh
3.5k
You can check the read lengths of each file to determine which one is the R1 and which is the R2. Also, check the 10x protocol version they…
Comment: Subsetting before QC in Spatial Transcriptomics
by
Kent
▴ 30
Hi Kevin, Thanks for the detailed explanation. Due to the characteristics of the datasets, we initially used very lenient quality control…
Comment: Midpoint rooting IQTREE newick file moves node support around
by
Luca Arbore
▴ 10
Thank you very much Kevin, it worked!
Comment: ID unifiying across different datasets
by
GenoMax
154k
In this case the entry notes that this is likely the product of a pseudogene: https://www.uniprot.org/uniprotkb/Q5VTE0/entry and existence …
Comment: Comparison of different RNAseq data sets
by
DrSmad
▴ 10
Each lab contributes both control and LPS. Example, for cell line A_lab1 did and analysis on control and LPS-6h. Cell line B_lab2 did contr…
Comment: ID unifiying across different datasets
by
zizigolu
★ 4.4k
sorry, why some gene names are often lacking though the Uniprot ID is still valid (using biomart)?
Comment: snpEff: Unsupported structural variant types
by
shpak.max
▴ 70
Unfortunately, while it ran without a problem initially, when I checked the run screen today, I saw the following error message (and unlike…
Comment: ID unifiying across different datasets
by
GenoMax
154k
You can use the [**ID mapping tool**][1] from UniProt site (third ID did not map from the list above): From To P68104 ENSG0000015…
Answer: The geo samples is not having sentrix id and sentrix position. But this informat
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yura.grabovska
▴ 890
Crosspost from related question: https://www.biostars.org/p/9616466/#9616534 ``` ##Using R, illuminaio from Bioconductor library(…
Answer: Finding Sentrix ID in HM450K arrays
by
yura.grabovska
▴ 890
``` ##Using R, illuminaio from Bioconductor library(illuminaio) temp.idat <- readIDAT(file = "200379120087_R02C02_Grn.idat") tem…
Comment: Can i use orthofinder for small protein datasets and not full proteome?
by
michael.ante
★ 4.0k
Do you want to compare them by sequence or by function? For the later, you can use e.g. InterProScan, KoFamScan.
Answer: Can i use orthofinder for small protein datasets and not full proteome?
by
dthorbur
★ 3.2k
If you're just using the tool for clustering purposes, I think OrthoFinder might be a little clunky and would recommend using something lik…
Comment: ID unifiying across different datasets
by
zizigolu
★ 4.4k
Thank you; The problem is let's say in the protein ID column I see `Q5VTE0;P68104;Q05639` here I am sure I should get which `ENSG` for eac…
Comment: How to improving 2-Nucleotide RNA-seq Mapping Accuracy
by
2411110159
• 0
Since we do not have real data yet, I tried to simulate this using strand-specific RNA bisulfite-seq reads (C to T). Read1 corresponds to t…
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by
2411110159
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