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1,000 results • Page
2 of 20
Sort: Rank
Rank
Views
Votes
Replies
1
vote
3
replies
187
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
1 day ago by
WouterDeCoster
47k
0
votes
3
replies
190
views
Help for coding: Trinity for differential gene expression studies
Gene
updated 1 day ago by
mchour
• 0 • written 1 day ago by
rhossen
• 0
1
vote
1
reply
144
views
WGCNA preservation analysis
WGCNA
preservation
updated 1 day ago by
Michael
54k • written 1 day ago by
michael.flower.14
▴ 180
1
vote
3
replies
224
views
some error in building kraken2 database
metagenome
kraken2
17 hours ago by
Art1ess
• 0
0
votes
1
reply
117
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 1 day ago by
bk11
★ 2.3k • written 1 day ago by
Susmita Mandal
▴ 110
0
votes
1
reply
120
views
Plots for DNA methylation data
plots
DNA
methylation
updated 1 day ago by
GenoMax
141k • written 1 day ago by
sarahawan92
▴ 10
0
votes
3
replies
473
views
python file for coding potential calculator
cpc2.py
updated 1 day ago by
atharvakarkare14
▴ 10 • written 6 days ago by
Ashok
• 0
1
vote
1
reply
150
views
Failed kmer content
kmer
illumina
ngs
updated 1 day ago by
Ram
43k • written 1 day ago by
Kasturi
• 0
0
votes
1
reply
184
views
Heatmap and rna-seq
RNA-Seq
Heatmap
and
updated 21 hours ago by
Istvan Albert
100k • written 1 day ago by
qudrat.nii
▴ 10
0
votes
0
replies
154
views
Forum:
Improvement on automatic annotation of single-cell RNA-seq data from the literature using LLM
annotation
scRNA
llm
1 day ago by
yxwucq
• 0
0
votes
0
replies
77
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 1 day ago by
Ram
43k • written 1 day ago by
SSSJec
• 0
0
votes
6
replies
279
views
How to slice a gvcf file with tabix?
Tabix
bed
gvcf
23 hours ago by
Sd
• 0
0
votes
2
replies
161
views
Help with Base quality Score Recalibration (BQSR) using GATK
GATK
BQSR
1 day ago by
sainavyav22
• 0
0
votes
1
reply
132
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 1 day ago by
Ram
43k • written 1 day ago by
Cameron.walker9900
• 0
0
votes
8
replies
271
views
Error in cnetplot enrichplot package
R
updated 1 day ago by
Ram
43k • written 2 days ago by
Farhad
• 0
3
votes
9
replies
375
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 6 hours ago by
Istvan Albert
100k • written 2 days ago by
Κοσμάς
• 0
0
votes
0
replies
102
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 2 days ago by
Ram
43k • written 2 days ago by
maxime.policarpo
▴ 200
3
votes
3
replies
171
views
Genbank vs SRA
ncbi
genbank
genomics
sra
updated 2 days ago by
Mensur Dlakic
★ 27k • written 2 days ago by
c_u
▴ 520
0
votes
0
replies
85
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 2 days ago by
Ram
43k • written 2 days ago by
sansan_96
▴ 80
0
votes
0
replies
90
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 1 day ago by
Ram
43k • written 2 days ago by
Amélie
• 0
0
votes
0
replies
132
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 2 days ago by
Ram
43k • written 2 days ago by
Oak
▴ 10
1
vote
3
replies
2.4k
views
Problem to remove subset of patients with plink
plink
PED
updated 1 day ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
2
votes
3
replies
178
views
from row count to tpm
tpm
row-count
normalization
1 day ago by
michelafrancesconi9
▴ 20
1
vote
5
replies
236
views
Downsampling fastq file
downsample
fastq
updated 2 days ago by
Ram
43k • written 2 days ago by
marco.barr
▴ 80
2
votes
3
replies
303
views
How to establish haplotype-specific gene expression levels
RNA-seq
Haplotype
updated 2 days ago by
dsull
★ 5.8k • written 15 days ago by
javanokendo
▴ 60
0
votes
1
reply
120
views
tbtool
tbtool
updated 2 days ago by
Ram
43k • written 2 days ago by
Raman
• 0
0
votes
2
replies
176
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 2 days ago by
i.sudbery
19k • written 2 days ago by
Patadu94
• 0
3
votes
3
replies
194
views
Getting the nucleotide sequence of proteins, having their UniProt IDs
Nucleotide
Genomic
Sequence
Uniprot
Proteins
updated 2 days ago by
GenoMax
141k • written 2 days ago by
Mariana
▴ 10
0
votes
2
replies
141
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 2 days ago by
Mensur Dlakic
★ 27k • written 2 days ago by
emmanouil.a
▴ 120
0
votes
1
reply
114
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 2 days ago by
ATpoint
82k • written 2 days ago by
enanoide
• 0
0
votes
0
replies
79
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
2 days ago by
manaswwm
▴ 490
3
votes
3
replies
707
views
KissDE and batch effect
kissDE
kissplice
2 days ago by
david.b.rombaut
▴ 10
0
votes
0
replies
69
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
1 day ago by
alifafiq1
• 0
76
votes
71
replies
19k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
updated 2 days ago by
GenoMax
141k • written 6.2 years ago by
Kevin Blighe
87k
0
votes
0
replies
78
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
2 days ago by
feather-W
• 0
2
votes
4
replies
235
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
11 hours ago by
samuelkalandarov2002
▴ 10
0
votes
0
replies
75
views
Annotating single cell data automatically
cell
annotation
single
2 days ago by
Gerard
• 0
0
votes
0
replies
76
views
News:
Online course: DNA methylation
Pacbio
Nanopore
DnaMethylation
Evolution
2 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
118
views
Job:
Ensembl Plants Senior Bioinformatician
ebi
embl
genomics
ensembl
2 days ago by
Ben_Ensembl
★ 2.4k
2
votes
4
replies
261
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
16 hours ago by
HyperEvo
• 0
0
votes
1
reply
137
views
RNA-seq bacteria contamination
RNA-seq
updated 2 days ago by
GenoMax
141k • written 2 days ago by
sh
• 0
0
votes
2
replies
174
views
Result of running of p3_in.pl
primer3
updated 2 days ago by
GenoMax
141k • written 2 days ago by
nasri
• 0
0
votes
1
reply
123
views
FAM FILE
file
Fam
2 days ago by
Eleonora
• 0
0
votes
0
replies
67
views
Imputation advice
imputation
2 days ago by
kl
▴ 10
3
votes
5
replies
234
views
Per base sequence content error in RNAseq analysis
RNA-seq
analysis
updated 2 days ago by
GenoMax
141k • written 2 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
83
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
2 days ago by
Enrique
• 0
3
votes
5
replies
527
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
2 days ago by
n_navy
• 0
0
votes
0
replies
69
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
2 days ago by
sativus
▴ 20
6
votes
3
replies
161
views
Interpretting IGV output
IGV
updated 2 days ago by
Carlo Yague
8.7k • written 2 days ago by
analyst
▴ 30
0
votes
1
reply
167
views
homology modelling using swiss model
homology-modeling
swiss-model
updated 2 days ago by
colindaven
6.4k • written 3 days ago by
Ayush
• 0
1,000 results • Page
2 of 20
Recent Votes
Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
Comment: To get p-values for the TPM
A: Where To Download Pam50 Gene Set?
A: Where To Download Pam50 Gene Set?
Answer: Fail to install umap-learn in R
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Recent Replies
Comment: Troubleshooting RNA-seq data with DNA contamination
by
DKA
▴ 40
I have unstranded RNA-seq data. Please share the tool with me, if you do not mind.
Comment: PCA plot (Suggestions Needed)
by
Mensur Dlakic
★ 27k
Everything that @f1f58aed said, plus that there may be no data manipulation that will give you the clusters you expected. Sometimes there a…
Answer: Creating Synthetic Sequences for a ML Model
by
Mensur Dlakic
★ 27k
It is a good idea, though I don't see how it would work in practice. I think you will encounter at least additional problem on top of da…
Answer: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
Right now, the WT samples are clustering together, but you have one mutant sample off by itself, which could be an outlier. How did you sc…
Comment: Adding CB tag to bam file
by
GenoMax
141k
@yokofakun had written this: https://www.biostars.org/p/336965/ https://github.com/ruqianl/appendCB may also be useful.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
GenoMax
141k
Please post information about your tool as a `tools` category post. Don't wait/ask other users to ask you.
Comment: Adding CB tag to bam file
by
Maria
• 0
Sorry for the delay in my answer, I got sidetracked. I am using ```samtools addreplacerg -r "@RG\tID:$cell" -o $cell.bam -h $LINE``` bu…
Answer: Troubleshooting RNA-seq data with DNA contamination
by
haibol2017
▴ 10
We just developed a R package to tackle this problem. Do you have stranded or unstranded RNA-seq data contaminated with gDNA? If you wou…
Comment: How to trim transcripts using information from NCBI contamination screen report
by
GenoMax
141k
`bbduk.sh` can use the transcripts as input. There is a `adapters.fa` included in the `resources` directory of the distribution. You can do…
Comment: PCA plot (Suggestions Needed)
by
swbarnes2
14k
Cross posted here (including the code used to make up the counts): https://support.bioconductor.org/p/9157911/#9157959
Comment: To get p-values for the TPM
by
swbarnes2
14k
RSEM returns a kind of p-value if you run it with the "prior-enhanced" option. Did you do that? Are you completely sure that's the value y…
Comment: How to trim transcripts using information from NCBI contamination screen report
by
Lada
▴ 30
i checked both of these programs (`bbduk` and `fastp`) and it seems they use reads as inputs (fastq formats)... how can I trim my transcrip…
Comment: AGeNT LocatIt
by
barslmn
★ 2.1k
He is already giving 32G, 320G for marking duplicates for exome is excessive. Is there a specific reason for using the tool?
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.3k
This looks good. Please try with using `--allow-no-sex flag` plink --bfile your_data_phenoUP --assoc --allow-no-sex --out your_data_ph…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
SC899359_PC75420_A05 SC899359_PC75420_A05 0 0 0 2 SC899360_PC75415_D01 SC899360_PC75415_D01 0 0 0 2 SC899361_PC75425_H05 SC899361_PC75425_H…
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