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116,582 results • Page
2 of 2332
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Votes
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1
vote
1
reply
146
views
Failed kmer content
kmer
illumina
ngs
updated 22 hours ago by
Ram
43k • written 1 day ago by
Kasturi
• 0
0
votes
1
reply
180
views
Heatmap and rna-seq
RNA-Seq
Heatmap
and
updated 15 hours ago by
Istvan Albert
100k • written 1 day ago by
qudrat.nii
▴ 10
0
votes
0
replies
152
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
76
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 22 hours ago by
Ram
43k • written 1 day ago by
SSSJec
• 0
0
votes
6
replies
274
views
How to slice a gvcf file with tabix?
Tabix
bed
gvcf
18 hours ago by
Sd
• 0
0
votes
2
replies
160
views
Help with Base quality Score Recalibration (BQSR) using GATK
GATK
BQSR
1 day ago by
sainavyav22
• 0
0
votes
1
reply
129
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
266
views
Error in cnetplot enrichplot package
R
updated 1 day ago by
Ram
43k • written 1 day ago by
Farhad
• 0
3
votes
9
replies
348
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 1 hour ago by
Istvan Albert
100k • written 1 day ago by
Κοσμάς
• 0
0
votes
0
replies
101
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 1 day ago by
Ram
43k • written 1 day ago by
maxime.policarpo
▴ 200
3
votes
3
replies
165
views
Genbank vs SRA
ncbi
genbank
genomics
sra
updated 1 day ago by
Mensur Dlakic
★ 27k • written 1 day ago by
c_u
▴ 520
0
votes
0
replies
84
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 1 day ago by
Ram
43k • written 1 day ago by
sansan_96
▴ 80
0
votes
0
replies
89
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 22 hours ago by
Ram
43k • written 1 day ago by
Amélie
• 0
0
votes
0
replies
131
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 1 day ago by
Ram
43k • written 1 day 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
177
views
from row count to tpm
tpm
row-count
normalization
1 day ago by
michelafrancesconi9
▴ 20
1
vote
5
replies
230
views
Downsampling fastq file
downsample
fastq
updated 1 day ago by
Ram
43k • written 1 day ago by
marco.barr
▴ 80
2
votes
3
replies
302
views
How to establish haplotype-specific gene expression levels
RNA-seq
Haplotype
updated 1 day ago by
dsull
★ 5.8k • written 14 days ago by
javanokendo
▴ 60
0
votes
1
reply
118
views
tbtool
tbtool
updated 1 day ago by
Ram
43k • written 1 day ago by
Raman
• 0
0
votes
2
replies
172
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 1 day ago by
i.sudbery
19k • written 1 day ago by
Patadu94
• 0
3
votes
3
replies
192
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
140
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 1 day ago by
Mensur Dlakic
★ 27k • written 2 days ago by
emmanouil.a
▴ 120
0
votes
1
reply
112
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
77
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
2 days ago by
manaswwm
▴ 490
3
votes
3
replies
706
views
KissDE and batch effect
kissDE
kissplice
2 days ago by
david.b.rombaut
▴ 10
0
votes
0
replies
68
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
77
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
222
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
5 hours ago by
samuelkalandarov2002
▴ 10
0
votes
0
replies
74
views
Annotating single cell data automatically
cell
annotation
single
2 days ago by
Gerard
• 0
0
votes
0
replies
75
views
News:
Online course: DNA methylation
Pacbio
Nanopore
DnaMethylation
Evolution
2 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
115
views
Job:
Ensembl Plants Senior Bioinformatician
ebi
embl
genomics
ensembl
2 days ago by
Ben_Ensembl
★ 2.4k
2
votes
4
replies
257
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
11 hours ago by
HyperEvo
• 0
0
votes
1
reply
136
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
173
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
117
views
FAM FILE
file
Fam
2 days ago by
Eleonora
• 0
0
votes
0
replies
66
views
Imputation advice
imputation
2 days ago by
kl
▴ 10
3
votes
5
replies
229
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
81
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
2 days ago by
Enrique
• 0
3
votes
5
replies
525
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
68
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
2 days ago by
sativus
▴ 20
6
votes
3
replies
159
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
166
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
0
votes
0
replies
74
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
2 days ago by
Biostars2200
• 0
1
vote
5
replies
282
views
DYH17 Structure Prediction
BLAST
Protein-Structure-Prediction
22 hours ago by
anasjamshed
▴ 120
0
votes
0
replies
114
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 2 days ago by
Carlo Yague
8.7k • written 2 days ago by
Atul K.
• 0
3
votes
2
replies
254
views
p-value and Boneferroni adjusted p-value the same in R
Bonferroni
R
Statistics
p-value
Fisher
2 days ago by
kristiewyleung
• 0
2
votes
5
replies
418
views
Marking duplicates using UMIs
Deduplication
UMI
updated 2 days ago by
i.sudbery
19k • written 3 days ago by
Lipika
• 0
0
votes
0
replies
134
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 2 days ago by
Ram
43k • written 3 days ago by
sainavyav22
• 0
0
votes
0
replies
136
views
Bacterial genome alignment with mauve
Bacteria
mauve
genome
3 days ago by
rthapa
▴ 90
116,582 results • Page
2 of 2332
Recent Votes
Comment: How to trim transcripts using information from NCBI contamination screen report
Difference Between "Mate Pair" And "Pair-End"
Difference Between "Mate Pair" And "Pair-End"
Comment: To get p-values for the TPM
Comment: HaplotypeCaller - only SNPs
Answer: To get p-values for the TPM
Comment: To get p-values for the TPM
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Recent Replies
Comment: How to trim transcripts using information from NCBI contamination screen report
by
Lada
▴ 30
Thank you and yes, I agree going step back is the best option but I am in a hurry at the moment so I just need to stick to the transcriptom…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
Thank you so much for helping me out! I did the steps you mentioned but still got the same issue as shown in the snapshot ![enter image des…
Comment: different FeatureCounts output for the same data
by
Istvan Albert
100k
Make sure you are using the same version of featureCounts, it has changed how it deals with paired end reads. The exact same command will p…
Comment: Wilcox test using data slot (log normalized count values) of scRNA-seq between t
by
mropri
▴ 150
Thank you, will do Wilcox for now as I only have one control and one treatment, as I get more control and treatment samples, will stick wit…
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
by
Istvan Albert
100k
I think the blog post lines up wit both of our statements. It seems that 2-way binning (pass/fail) already dramatically improves the calls…
Comment: Tax4Fun2 - error
by
drstalinantony28
• 0
You have to follow this step to solve the issue. (Mostly this problem occurs in the Windows version) 1. If you are using R studio in Windo…
Answer: Tax4Fun2 - error
by
drstalinantony28
• 0
You have to follow this step to solve the issue. (Mostly this problem occurs in the Windows version) 1. If you are using R studio in Win…
Comment: different FeatureCounts output for the same data
by
GenoMax
141k
> featureCounts alignment rate is only around 15-20%. You mean assignment rate? It is that low even after allowing for counting of multi-m…
Comment: alignment result
by
GenoMax
141k
> 20386810 (88.67%) aligned concordantly exactly 1 time This result is fine.
Comment: To get p-values for the TPM
by
ATpoint
82k
Seconding that. Just use established pipelines, tximport => DESeq2, get your stats and call it a day. Custom pipelines paired with little e…
Comment: Should I remove unlocalized scaffols in reference genome before alignment?
by
njornet
▴ 20
I don't want reads incorrectly aligned to these scaffolds and loose information of relevant regions, but as you said that probably won't ha…
Comment: To get p-values for the TPM
by
dsull
★ 5.8k
Your post should be a "com, not an "answer". Use "Add Comment" to request clarifications on an answer someone has provided. tximport can t…
Comment: Use of Kraken output for functional analysis
by
gv
• 0
Hello, you can use kraken-biom [kraken_biom.py] tool to get your Biom file from input kreport cheers,
Comment: To get p-values for the TPM
by
VITALA
• 0
sir, deseq2 takes counts as inputs rightfor the hypothesis testing /to see the variance between the two groups, but in my case what i want …
Answer: To get p-values for the TPM
by
dsull
★ 5.8k
There are plenty of RSEM -> tximport -> DESeq2 tutorials online. Just follow one of those. DESeq2 will give you "p values" based on a Wa…
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