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119,774 results • Page
1 of 2396
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
46
views
Deducing AIRR-seq Library Generation From SRA Data
SRA
generation
airflow
primer
airrflow
10 hours ago by
A Soggy Waffle
• 0
0
votes
0
replies
74
views
STAR pair-end gene count discrepancy vs. RSEM
rsem
htseqcount
star
genecount
13 hours ago by
cropero
• 0
0
votes
2
replies
283
views
How to remove duplicated SNPs based on MAF with Plink?
SNPs
Plink2
duplication
maf
updated 18 hours ago by
hakimbazol
▴ 20 • written 4 days ago by
giulia.trauzzi
▴ 30
0
votes
1
reply
106
views
linear pangenome for crops
pangenome
linear
updated 5 hours ago by
Semir
▴ 20 • written 20 hours ago by
analyst
▴ 50
820
votes
169
replies
160k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 11 weeks ago by
Biostar
3.2k • written 8.0 years ago by
Istvan Albert
102k
0
votes
0
replies
70
views
Can we construct single pangenome for different crops
pangenome
different
crops
20 hours ago by
analyst
▴ 50
0
votes
0
replies
106
views
Is it possible to get the percentage identity between a pair of orthologs at the proteome level with the Orthology Matrix (OMA)?
with
OMA
Sequence
identity
updated 5 hours ago by
GenoMax
148k • written 20 hours ago by
fcampbel
• 0
0
votes
0
replies
97
views
On applying spike-in-derived scaling factors to ChIP-seq data: adjust for background signal (input) or not?
spike-in
deepTools
normalization
ChIP-seq
scaling-factor
1 day ago by
kalavattam
▴ 280
0
votes
2
replies
270
views
model interaction in DeSeq2 with >1K samples
DeSeq2
interaction
large
sample
set
design
updated 1 day ago by
i.sudbery
20k • written 2 days ago by
L.Grigoreva
• 0
0
votes
1
reply
163
views
Single Copy lncRNA
lncRNA
Single
Copy
updated 1 day ago by
Semir
▴ 20 • written 1 day ago by
Kutti
• 0
1
vote
6
replies
369
views
Concatenating all unmapped or alternative contigs in a reference genome
contigs
fasta
reference
updated 1 day ago by
Semir
▴ 20 • written 2 days ago by
manikin_python9f
• 0
0
votes
3
replies
275
views
Feature Counts - potential bug with outfile.jcounts
Feature
Gordon
Smyth
Counts
updated 1 day ago by
GenoMax
148k • written 1 day ago by
chrisk
• 0
0
votes
1
reply
222
views
log transformation before imputation (impute.knn) in proteomic data?
proteomic
log_transformation
impute.knn
updated 1 day ago by
KABILAN
▴ 130 • written 2 days ago by
Lila M
★ 1.3k
0
votes
2
replies
216
views
Spatial correlation between two continuous variables
spatial
transcriptomics
correlation
updated 1 day ago by
dsull
★ 6.9k • written 2 days ago by
hossiny
• 0
5
votes
6
replies
451
views
IGV is not showing all alignments of SAM file
IGV
2 days ago by
gernophil
▴ 120
1
vote
6
replies
321
views
Multimapping Reads to be counted or not
lowcounts
featureCounts
RNASeq
Multimapping
updated 2 days ago by
GenoMax
148k • written 2 days ago by
rajdeepboral00
• 0
0
votes
1
reply
202
views
How to create modified basecalling dataset with nanopore data with an ambiguous motif sequence?
dorado
nanopore
remora
updated 2 days ago by
GenoMax
148k • written 2 days ago by
swim1128
• 0
0
votes
2
replies
200
views
How to visualize shared pathways between ORA (enrichment) results?
visualization
ora
pathways
enrichment
2 days ago by
Picasa
▴ 650
4
votes
2
replies
230
views
How Can Pathway Analysis Methods Account for Genes with Different Activation Roles?
gsea
functional-analysis
pathway-enrichment
updated 2 days ago by
GenoMax
148k • written 2 days ago by
RoyBatty
▴ 30
0
votes
1
reply
160
views
miRNA analysis
miRNA
vescicles
extracellular
updated 2 days ago by
biofalconch
★ 1.3k • written 2 days ago by
deniselavezzari
• 0
3
votes
1
reply
229
views
tRNA nomenclature / numbering conventions
tRNA
RNAseq
updated 2 days ago by
microfuge
★ 2.0k • written 3 days ago by
noodle
▴ 590
0
votes
2
replies
214
views
Where can I get gtf file for Adenovirus 5?
gtf
files
virus
2 days ago by
new
▴ 10
0
votes
3
replies
287
views
Understanding STARsolo --soloStrand values and 10X scRNA-seq library structure
10X
scRNA-seq
stranded
updated 1 day ago by
dsull
★ 6.9k • written 3 days ago by
mk
▴ 300
1
vote
2
replies
186
views
The quality of the linear reference genome used for constructing a pan-genome
cactus-minigraph
2 days ago by
chiyong4783
• 0
1
vote
2
replies
329
views
HLA alignment, approximation and frequencies
Fastq
1 day ago by
oumo
• 0
0
votes
5
replies
1.0k
views
Convert RNASeq V2 data in cBioPortal having RSEM normalized results to TPM values
TPM
RNA-Seq
cbioportal
RSEM
updated 1 day ago by
dsull
★ 6.9k • written 14 months ago by
shakyaram079
• 0
0
votes
0
replies
118
views
Mutational Signatures, General Standard Refit, Cosine similarity
Standard
Refit
selected
in
signatures
2 days ago by
shakyaram079
• 0
1
vote
1
reply
187
views
Dorado for m6A modification detection
dorado
m6A
nanopore
updated 2 days ago by
GenoMax
148k • written 2 days ago by
baibhu1234
• 0
0
votes
17
replies
1.2k
views
7 follow
The BUSCO assessment of the MAKER annotation results shows a low completeness
BUSCO
MAKER
updated 2 days ago by
Michael
55k • written 4 weeks ago by
mut
• 0
0
votes
2
replies
194
views
Create custom references for Macaca fascicularis using Cellranger -arc
fascicularis
references
Cellranger
Macaca
custom
-arc
2 days ago by
tranhangk15cnsh
• 0
0
votes
2
replies
235
views
vg mod changes a graph, but what about a gam or gamp to the original graph?
vg
1 day ago by
joseph.fass
▴ 10
0
votes
3
replies
448
views
Getting an Expression Matrix from GDC Manifest File
RNAseq
updated 3 days ago by
Zhenyu Zhang
★ 1.2k • written 17 days ago by
cthangav
▴ 110
0
votes
5
replies
433
views
Scale-free topology fit index WGCNA
unsigned
signed
WGCNA
updated 18 hours ago by
andres.firrincieli
3.8k • written 5 days ago by
cropero
• 0
0
votes
1
reply
187
views
RNA seq analysis in R
R
pca
heatmap
updated 3 days ago by
jared.andrews07
★ 18k • written 3 days ago by
anasjamshed
▴ 140
3
votes
0
replies
181
views
Herald:
The Biostar Herald for Thursday, December 05, 2024
herald
3 days ago by
Biostar
3.2k
0
votes
0
replies
134
views
How to get the differential abundant taxa of the first time point in time series analysis
LRT
3 days ago by
leranwangcs
▴ 150
0
votes
2
replies
211
views
Sequence duplication in fastqc
fastqc
duplication
RNASeq
3 days ago by
rajdeepboral00
• 0
4
votes
6
replies
300
views
Forum:
How do I start my journey as bioinformatics?
Student
Education
Career
Bioinformatics
Programming
updated 3 days ago by
jared.andrews07
★ 18k • written 3 days ago by
khumza050
• 0
0
votes
0
replies
125
views
Mice DEGs for SBGNview plot
SBGNview
RNA-seq
DEGs
mice
3 days ago by
alwayshope
▴ 40
1
vote
4
replies
937
views
Motif Scanning: HOMER vs MEME, settings?
homer
fimo
updated 3 days ago by
LChart
4.6k • written 8 months ago by
mb
• 0
12
votes
9
replies
503
views
7 follow
Best Approach to Identify Human-C. elegans Orthologs?
c.elegans
Orthologs
Homologs
Genomics
2 days ago by
bioinformatics_rk
• 0
3
votes
3
replies
244
views
How to retain interactive plots from Glimma in R Markdown HTML Document
R
glimma
markdown
updated 3 days ago by
yura.grabovska
▴ 690 • written 3 days ago by
soullevram98
▴ 10
4
votes
11
replies
590
views
Counts after using feature counts is low
hisat2
featureCounts
lowcounts
updated 3 days ago by
GenoMax
148k • written 4 days ago by
rajdeepboral00
• 0
2
votes
6
replies
351
views
PCA interpretation
RNASeq
PCA
updated 2 days ago by
KABILAN
▴ 130 • written 3 days ago by
nuriagaralon
▴ 20
1
vote
3
replies
271
views
samtools reheader error
samtools
updated 3 days ago by
aw7
▴ 350 • written 3 days ago by
chiyong4783
• 0
0
votes
0
replies
180
views
Job:
Postdoctoral Research Associate
postdoc
3 days ago by
Ta-Chiang
• 0
2
votes
2
replies
266
views
Paired End Data Merging: Before Or After ?
Workflow
Merging
Paired
Metagenomics
Fastq
3 days ago by
Aytaç
• 0
0
votes
0
replies
166
views
Small Molecule Databases and clustering
polyethylene
MolecularDatabase
Molecule
PET
trephthalate
4 days ago by
yarrowmadrona
▴ 10
0
votes
2
replies
545
views
Computational tools for predicting novel substrates for a class of enzymes
substrate
catalysis
enzyme
4 days ago by
yarrowmadrona
▴ 10
3
votes
2
replies
264
views
biomart hangs
biomaRt
updated 3 days ago by
Mark
★ 1.6k • written 4 days ago by
ramiro.barrantes
• 0
119,774 results • Page
1 of 2396
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How Can Pathway Analysis Methods Account for Genes with Different Activation Roles?
Effect of Bootstrapping/Gibbs Sampling in Salmon Counts
Comment: HLA alignment, approximation and frequencies
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Comment: SnpEff Query
Merging CRAM files
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Comment: linear pangenome for crops
by
Semir
▴ 20
You can use Cactus to do so: cactus-align ./jobstore \ seqFile.txt \ alignment.maf \ --reference ${reference_g…
Comment: How to remove duplicated SNPs based on MAF with Plink?
by
Semir
▴ 20
# Calculate allele frequencies for all variants plink2 --pfile ${input_prefix} \ --freq \ --out ${params.outp…
Comment: Looking for a mentor in bioinformatics with animal selection specialization
by
biology.may20
▴ 20
thank you Felix, glad to write to you
Comment: Scale-free topology fit index WGCNA
by
andres.firrincieli
3.8k
Without the Sep 5, there is an improvement, at least for the unsigned network. The mean connectivity (mean.k.) is a little bit too high but…
Comment: How to remove duplicated SNPs based on MAF with Plink?
by
hakimbazol
▴ 20
Since the MAF values are different, is it possible to filter your result based on MAF first? And then see whether the duplicates are still …
Comment: Single Copy lncRNA
by
Semir
▴ 20
I think you should be able to use Blast # Create BLAST database makeblastdb \ -in ${input_fasta} \ -dbtype nucl \ …
Answer: model interaction in DeSeq2 with >1K samples
by
i.sudbery
20k
In their discussion of doing single cell RNAseq, which also often has a large number of samples, the DESeq2 authors recommend using glmGamP…
Answer: Concatenating all unmapped or alternative contigs in a reference genome
by
Semir
▴ 20
I'd also like to share an alternative answer that might be less cryptic than the sed command: # First concatenate all fa files in th…
Comment: Feature Counts - potential bug with outfile.jcounts
by
GenoMax
148k
Tagging https://www.biostars.org/u/13578/ <!-- this is nothing -->
Comment: HLA alignment, approximation and frequencies
by
oumo
• 0
Thank you Let me check out these specialized tools
Comment: Feature Counts - potential bug with outfile.jcounts
by
chrisk
• 0
Thanks for the comment @GenoMax. We too note, those genes are on opposite strands. For context, we have an unstranded library. Cheers, C…
Comment: Feature Counts - potential bug with outfile.jcounts
by
GenoMax
148k
These two genes are on opposite strands. Based on your command you appear to have unstranded data or are doing the counting with that setti…
Comment: Refseq1405.40 and hisat2-build (-ss and --exon)
by
chrisk
• 0
Hello Biostars community, For anyone else whom this issue may concern, It was obviated with a bare metal install of Linux. We did not hea…
Answer: log transformation before imputation (impute.knn) in proteomic data?
by
KABILAN
▴ 130
By which normalization method you have applied to the dataset? Since normalization and imputation methods are data-specific in nature, yo…
Answer: Spatial correlation between two continuous variables
by
dsull
★ 6.9k
Looks at bivariate metrics like Lee’s L https://link.springer.com/article/10.1007/s101090100064
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