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324 results • Page
2 of 7
Sort: Votes
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Votes
Replies
1
vote
3
replies
274
views
DNA/RNA Sequence Alignment
dna
rna
alignment
sequence
updated 16 days ago by
Mensur Dlakic
★ 25k • written 16 days ago by
Mirza
• 0
1
vote
1
reply
1.4k
views
Star alignment - AS and MD tags
alignment
ngs
Star
SAM format
SAM alignment tags
updated 28 days ago by
xiaoleiusc
▴ 120 • written 3.6 years ago by
mickey_95
▴ 100
1
vote
3
replies
273
views
PMID multiple pdfs download using R
R
PubMed
updated 17 days ago by
Ram
41k • written 18 days ago by
Confused_human
▴ 10
1
vote
2
replies
321
views
Issues with Mixture file when using CIBERSORTx
Deconvolution
CIBERSORTx
updated 14 days ago by
Hongjin
• 0 • written 8 weeks ago by
mateomejias
• 0
1
vote
1
reply
529
views
fragments.tsv.gz file in ATAC seq
ATAC-seq
updated 5 days ago by
tingting
▴ 10 • written 8 months ago by
Chris
▴ 230
1
vote
1
reply
168
views
Harmony integration PC variance explained
scRNA
integration
harmony
updated 3 days ago by
CTLong
▴ 20 • written 5 days ago by
e.iich
• 0
1
vote
7
replies
587
views
help with weird PCA? (vcfR)
vcftools
vcfR
R
21 days ago by
MaeBH
• 0
1
vote
1
reply
186
views
Match variants for allele frequency, LD score, and other features
snp
2 days ago by
Jautis
▴ 520
1
vote
2
replies
247
views
Quality control on imputed genotypes for GWAS / application of PGS
qc
imputation
plink
regenie
gwas
18 days ago by
loy_loy
▴ 10
1
vote
2
replies
281
views
A question about the missing or not observed alleles in PLINK datasets
PLINK
14 days ago by
abedkurdi10
▴ 190
1
vote
8
replies
519
views
DESEQ2 design in DESeqDataSetFromMatrix: cell and treatment
rna-seq
deseq2
12 days ago by
pingu77
▴ 20
1
vote
2
replies
261
views
How to remove batch effect in RNA-seq using control samples?
Batch-effect
RNA-seq
11 days ago by
AS20
▴ 10
1
vote
2
replies
413
views
Beginner needing help interpreting these articles
Machine-learning
updated 25 days ago by
Ram
41k • written 15 months ago by
Ryan
• 0
1
vote
1
reply
198
views
Model matrix confront 2 groups out of 3
modelmatrix
r
designformula
deseq2
drimseq
updated 13 days ago by
ATpoint
78k • written 13 days ago by
dylannicoembros
• 0
1
vote
6
replies
521
views
frequency plot for peaks
chip-seq
chipseeker
updated 3 days ago by
Ankit
▴ 400 • written 18 days ago by
Mehwish
▴ 10
1
vote
3
replies
2.2k
views
BBMap : NH:i:1 and XT:A:R
bbmap
updated 10 days ago by
ayaosama2111
▴ 10 • written 7.1 years ago by
Nicolas Rosewick
10k
1
vote
1
reply
194
views
Transcript count normalization using Deseq2
transcript
DESeq2
updated 26 days ago by
ATpoint
78k • written 26 days ago by
Aiswarya
▴ 10
1
vote
4
replies
304
views
Analyze with Geo2R
R
NCBI
8 days ago by
anasjamshed
▴ 120
1
vote
5
replies
331
views
bcftools mipileup error: format error, unexpected A at line 1
bcftools
updated 18 days ago by
Jautis
▴ 520 • written 19 days ago by
jiyoung
▴ 20
1
vote
3
replies
296
views
How to find transcription factor in my gene set
transcription-factor
updated 29 days ago by
Ram
41k • written 29 days ago by
Ishak
• 0
1
vote
2
replies
204
views
Problem in installing 'magick' R package
R
installation
package
magick
updated 3 days ago by
DBScan
▴ 210 • written 3 days ago by
applepie
• 0
1
vote
4
replies
412
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
15 days ago by
Daniel
▴ 30
1
vote
2
replies
358
views
Bulk RNAseq Salmon index building which transcriptome to use
Salmon
RNA-seq
23 days ago by
Orange
▴ 10
1
vote
4
replies
377
views
Efficient Bulk Data Retrieval from NCBI BioProject
ncbi
SRAtoolkit
prefetch
14 days ago by
George
• 0
1
vote
2
replies
210
views
How to identify the nearest gene associated with a specific SNPs?
RSID
GWAS
updated 10 days ago by
Jeremy
▴ 850 • written 10 days ago by
camillab.
▴ 150
1
vote
6
replies
490
views
Parsing XML file from dbGaP
XML
26 days ago by
CTLong
▴ 20
1
vote
1
reply
177
views
RepeatModeler-2.0 BuildDatabase error
BuildDatabase
RepeatModeler
updated 17 days ago by
shelkmike
★ 1.1k • written 18 days ago by
1041853545
• 0
1
vote
0
replies
100
views
Visualize and explore eventalign data against reference
igv
minimap
nanopolish
nanopore
ngs
4 days ago by
joe
▴ 420
1
vote
1
reply
200
views
How to properly quantify gene expression of tandem duplicates from RNA-seq
pipeline
illumina
plants
RNA-seq
updated 19 days ago by
dthorbur
▴ 890 • written 19 days ago by
missTique
• 0
1
vote
4
replies
274
views
Bowtie mapping for single_end read
bowtie
3 days ago by
Rita
• 0
1
vote
3
replies
362
views
Differential Gene Expression between patients and not groups
differential-gene-expression
voom
limma
updated 26 days ago by
rpolicastro
12k • written 26 days ago by
Manuel
▴ 10
1
vote
0
replies
217
views
Convert Seurat object to anndata
anndata
h5ad
Seurat
18 days ago by
nadammagdy
▴ 10
1
vote
4
replies
288
views
Deseq2 5 level condition - building contrast
rna-seq
deseq2
updated 10 days ago by
ATpoint
78k • written 10 days ago by
annaA
▴ 10
1
vote
2
replies
231
views
ComBat-seq problem
ComBat-seq
RNA-Seq
batch-effect
updated 16 days ago by
Ram
41k • written 17 days ago by
Akash D
▴ 40
1
vote
3
replies
269
views
Identify clusters of populations based on gene expression
Seq
Single
cell
RNA
updated 3 days ago by
Nitin Narwade
★ 1.5k • written 4 days ago by
Bine
▴ 50
1
vote
6
replies
355
views
Discrepancy in total number of bases in trimmed read1 and read2 files after BBDuk
bbduk
3 days ago by
CTLong
▴ 20
1
vote
2
replies
202
views
DOES MGI SEQUENCING RESULT CONTAINS MULTIPLE FILES FOR SINGLE SAMPLE
whole
genome
assembly
sequencing
updated 9 days ago by
WouterDeCoster
47k • written 9 days ago by
manaswiniparija3
▴ 10
1
vote
1
reply
208
views
Fetch best fitted ligand from PDB
Structural-database
PDB
26 days ago by
yhdist
▴ 70
0
votes
0
replies
125
views
facing Issue while runing the CORASON command line
CORASON
families
BiG-SCAPE
gene
cluster
25 days ago by
kirankumareripogu
▴ 10
0
votes
0
replies
126
views
Retrieving NM:i edit distance field in .sam files generated by vg giraffe and vg surject
giraffe
surject
vg
10 days ago by
cassiwatt
• 0
0
votes
1
reply
262
views
WGCNA
WGCNA
p-value
updated 21 days ago by
jv
★ 1.2k • written 22 days ago by
hellokwmin
• 0
0
votes
0
replies
130
views
Tool similar to Centrifuge for bisulfite treated DNA
methylation
metagenomics
WGBS
26 days ago by
Carlos
• 0
0
votes
0
replies
83
views
How to find promoters (such as GC box and TATA box) in set of genes using bioinformatics analysis ?
motifs
promoters
bioinformatics
21 hours ago by
shome
▴ 10
0
votes
0
replies
117
views
Merging multiple DCC objects from multiple DSP runs
Spatial
transcriptomics
batches
DCC
GeoMx
16 days ago by
Pac314
▴ 10
0
votes
0
replies
115
views
Pathview Enzyme Code to Gene Symbol Conversion
Pathview
KEGG
11 days ago by
B.N.
• 0
0
votes
0
replies
72
views
is there a way to set colors pallets for glMDSPlot(x)?
Glimma
glMDSPlot
18 hours ago by
James
• 0
0
votes
0
replies
142
views
Dereplication of nanopore sequences using q2ONT workflow
qiime2
dereplication
27 days ago by
muhammad.akram
▴ 10
0
votes
0
replies
106
views
Population study based on metaT and MetaG
metagenome
metatranscriptome
study
population
updated 3 days ago by
GenoMax
136k • written 3 days ago by
PierreGT
• 0
0
votes
5
replies
452
views
bam file missing barcode and UMI info
barcode
star
starsolo
updated 22 days ago by
GenoMax
136k • written 25 days ago by
malonzm1
• 0
0
votes
3
replies
400
views
percentage of cells in each cluster- Seurat
seurat
updated 11 days ago by
seidel
11k • written 14 days ago by
odi
▴ 10
324 results • Page
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Recent Votes
Comment: How Can I move the scattered dots more closer into the center of box ?
Answer: How to compare two Seurat object (sample) in order to find top markers?
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Comment: Problematic fastq files...How can we trust them?
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Comment: Using metagenome assembly and binning to identify and mitigate contamination in
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Answer: Is bisulfite-seq data from different studies comparable with each other?
by
NextGenSeek
• 0
The efficiency of bisulfite treatment itself can differ significantly, so I would definitely not compare bisulfite-seq data from different …
Answer: Issue with genetic QC sex check
by
kl
▴ 10
After setting set-hh-missing, I have the following boxplot, where a F statistic of 0.91 corresponds to a female in my phenotypic dataset wh…
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78k
Converting data from one to another format and repairing gene names turned dates. Yes, great field.
Comment: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates with
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GenoMax
136k
Yes that should be true. I will let https://www.biostars.org/u/14684/ confirm.
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Gama313
▴ 120
Thanks for the answe and the linkI used bioinfokit tpm formula to calculate tpm from bulk which is the same formula given in your link: …
Comment: From TPM to raw counts
by
Gama313
▴ 120
Thanks Brian for the suggestion. However, I did the whole process, from bulk counts generation, to data transformation and scrna deconvolut…
Answer: Are 10x cellranger-arc ATAC bam files deduplicated?
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swbarnes2
13k
My experience with regular 10x bam files is that duplicates are not removed, but they are flagged as duplicates. So take a look at the …
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo
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fluke
• 0
Thanks a lot for your answer, I’m confused between RSEM expected count and RSEM normalized count. I’m working on this dataset from UCSC ht…
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Istvan Albert
99k
In principle, the TPM formula can be reverted, see the timeless post * [What the FPKM? A review of RNA-Seq expression units][1] In p…
Comment: Low coverage whole genome sequencing reveal excess heterozygosity for multiple S
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beausoleilmo
▴ 560
You're right, I wasn't explaining the problem clearly. Thanks for the directions! - The depth; coverage ~3.00X ± 2.50 SD - The sequen…
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
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Mensur Dlakic
★ 25k
All good points, especially about multiple copies of single-copy genes. I am doing error-correction in my assemblies, but was making an edu…
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo
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CTLong
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Yes, normalized RSEM counts from TCGA can be used as input for Limma Voom. Please check this post https://support.bioconductor.org/p/63981/…
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Sorry for the delay in expressing my thanks. I found the advice to look at the information from MySQL very useful. I will also refer to t…
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I'm posting this as a comment instead of an answer specifically because it's just what I would do and I don't know if it's the best approac…
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19k
In most cases error-correction should take care of error-spawned fake minor alleles, though... > If you want to convince yourself of this,…
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