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195 results • Page
2 of 4
Sort: Views
Rank
Views
Votes
Replies
3
votes
8
replies
455
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 14 hours ago by
swbarnes2
14k • written 1 day ago by
Aaliya
▴ 10
2
votes
5
replies
439
views
Marking duplicates using UMIs
Deduplication
UMI
updated 3 days ago by
i.sudbery
19k • written 4 days ago by
Lipika
• 0
0
votes
6
replies
424
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 1 day ago by
gv
• 0 • written 24 days ago by
Srinka
▴ 20
0
votes
2
replies
420
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
6 days ago by
_quantum_girl_
▴ 10
2
votes
2
replies
413
views
Using vg gamsort with naive sorting algorithm
gamsort
vg
updated 2 days ago by
Pierre Lindenbaum
161k • written 8 months ago by
AshleeThomson
▴ 80
1
vote
1
reply
412
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 4 days ago by
Gordon Smyth
★ 7.0k • written 7 days ago by
Chris
▴ 260
0
votes
2
replies
410
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
6 days ago by
Ashok
• 0
1
vote
1
reply
410
views
Plink merge errors.
cygwin64
bed
PLINK
6 days ago by
Dinmukhamed
• 0
1
vote
4
replies
408
views
GTF file for Rhinolophus sinicus
Rhinolophus-sinicus
GTF
updated 1 day ago by
atowns21
• 0 • written 5 months ago by
ara
• 0
3
votes
9
replies
405
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 1 day ago by
Istvan Albert
100k • written 3 days ago by
Κοσμάς
• 0
0
votes
10
replies
395
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
1 day ago by
atowns21
• 0
1
vote
1
reply
394
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
6 days ago by
renan.igor
• 0
4
votes
7
replies
375
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 10 hours ago by
dsull
★ 5.8k • written 1 day ago by
VITALA
• 0
0
votes
2
replies
372
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
6 days ago by
Ashok
• 0
0
votes
1
reply
363
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 4 hours ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
0
votes
3
replies
363
views
How to identify gaps in a genome?
awk
seqkit
assembly
fasta
genome
updated 2 days ago by
colindaven
6.4k • written 10 days ago by
rj.rezwan
• 0
2
votes
3
replies
310
views
How to establish haplotype-specific gene expression levels
RNA-seq
Haplotype
updated 3 days ago by
dsull
★ 5.8k • written 16 days ago by
javanokendo
▴ 60
1
vote
5
replies
306
views
DYH17 Structure Prediction
BLAST
Protein-Structure-Prediction
2 days ago by
anasjamshed
▴ 120
1
vote
1
reply
295
views
GTF file from Stringtie to R Studio for either Ballgown or DESeq2
Stringtie
Cufflinks
Ballgown
DESeq2
updated 5 days ago by
Ram
43k • written 5 days ago by
Nina
• 0
0
votes
8
replies
293
views
Error in cnetplot enrichplot package
R
updated 2 days ago by
Ram
43k • written 3 days ago by
Farhad
• 0
0
votes
6
replies
292
views
How to slice a gvcf file with tabix?
Tabix
bed
gvcf
1 day ago by
Sd
• 0
2
votes
1
reply
284
views
Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
shotgun
metagenomics
blastp
taxonomy
updated 5 days ago by
GenoMax
141k • written 5 days ago by
rebecca.calvo
• 0
0
votes
1
reply
281
views
Could you please assist in identifying this cluster?
single-cell
updated 6 days ago by
Ram
43k • written 6 days ago by
Kazo
• 0
0
votes
5
replies
280
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
1 day ago by
njornet
▴ 20
2
votes
4
replies
280
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
1 day ago by
HyperEvo
• 0
0
votes
4
replies
275
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
updated 1 day ago by
swbarnes2
14k • written 3 days ago by
dxj294
• 0
0
votes
0
replies
273
views
Choice of relatedness cutoff for GWAS of a large cohort (>100K samples)
relatedness
IBD
GWAS
updated 3 days ago by
Ram
43k • written 14 months ago by
Oak
▴ 10
3
votes
2
replies
266
views
p-value and Boneferroni adjusted p-value the same in R
Bonferroni
R
Statistics
p-value
Fisher
3 days ago by
kristiewyleung
• 0
0
votes
3
replies
264
views
Heatmap and rna-seq
RNA-Seq
Heatmap
and
updated 17 hours ago by
Kevin Blighe
87k • written 2 days ago by
qudrat.nii
▴ 10
0
votes
1
reply
259
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 6 days ago by
GenoMax
141k • written 6 days ago by
bioyas
▴ 10
0
votes
2
replies
258
views
bam merging for archaic samples
samtools
bam
updated 4 days ago by
Ram
43k • written 5 days ago by
Matteo Ungaro
▴ 100
2
votes
3
replies
255
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 3 days ago by
Mensur Dlakic
★ 27k • written 3 days ago by
emmanouil.a
▴ 120
1
vote
1
reply
254
views
Removing Illumina microarray probes with no expression HumanHT-12v4
microarray
HumanHT-12v4
Illumina
updated 5 days ago by
Gordon Smyth
★ 7.0k • written 5 days ago by
Bioinformatician
• 0
0
votes
5
replies
254
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 6 hours ago by
GenoMax
141k • written 1 day ago by
Bertalan_Takacs
▴ 90
1
vote
5
replies
252
views
Downsampling fastq file
downsample
fastq
updated 3 days ago by
Ram
43k • written 3 days ago by
marco.barr
▴ 80
7
votes
2
replies
252
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 1 day ago by
geneontologyhelp
▴ 390 • written 3 days ago by
catherine.teyssier
• 0
3
votes
5
replies
251
views
Per base sequence content error in RNAseq analysis
RNA-seq
analysis
updated 3 days ago by
GenoMax
141k • written 3 days ago by
ahmad.sajad4541
• 0
2
votes
4
replies
250
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
1 day ago by
samuelkalandarov2002
▴ 10
2
votes
4
replies
237
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
updated 1 day ago by
GenoMax
141k • written 2 days ago by
Lada
▴ 30
1
vote
3
replies
235
views
some error in building kraken2 database
metagenome
kraken2
1 day ago by
Art1ess
• 0
0
votes
4
replies
231
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
10 hours ago by
sehriban.buyukkilic
▴ 10
1
vote
2
replies
228
views
permutation test in edgeR
rna-seq
edgeR
updated 3 days ago by
Gordon Smyth
★ 7.0k • written 17 days ago by
Netanel
• 0
0
votes
2
replies
227
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 1 day ago by
Ram
43k • written 1 day ago by
v.berriosfarias
▴ 140
0
votes
3
replies
226
views
Difference between samtools "-f 9" and "-f 11"
samtools
sam
bam
updated 1 day ago by
Istvan Albert
100k • written 2 days ago by
Dylan
• 0
0
votes
0
replies
213
views
create genewise sync file in popoolation
popoolation
updated 6 days ago by
GenoMax
141k • written 6 days ago by
N.Y.Wiyana-Hewage
• 0
0
votes
0
replies
211
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
5 days ago by
abhishekghadge
• 0
3
votes
3
replies
209
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 2 days ago by
GenoMax
141k • written 2 days ago by
Estevão
• 0
3
votes
3
replies
207
views
Getting the nucleotide sequence of proteins, having their UniProt IDs
Nucleotide
Genomic
Sequence
Uniprot
Proteins
updated 3 days ago by
GenoMax
141k • written 3 days ago by
Mariana
▴ 10
0
votes
0
replies
203
views
Copy number variation plot
Copy-number-variation
genomics
updated 6 days ago by
Ram
43k • written 6 days ago by
Emmi
• 0
0
votes
0
replies
202
views
traying to make a maf from an already annotated vcf
vcf
vcf2maf
maf
maftools
VEP
3 days ago by
Javier
• 0
195 results • Page
2 of 4
Recent Votes
Answer: Sequence read length shorter than flow cell specification
Answer: Sequence read length shorter than flow cell specification
Comment: Why gatk VariantAnnotator required bam and coverage files
A: Generate Vcf.Gz File And Its Index File Vcf.Gz.Tbi
Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
Answer: How do I get the 3bp sequence on either side of a co-ordinate
What is the difference between HaplotypeCaller and UnifiedGenotyper?
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Recent Replies
Comment: Why gatk VariantAnnotator required bam and coverage files
by
QX
• 0
thank you!
Comment: Treatment VS Control in Single Cell RNAseq analysis
by
kilcdincer
▴ 10
Hello, I have more or less same experimental setting and was wondering how you proceeded with your analysis? Can I reach its GitHub reposit…
Comment: BLAST using both nucleotides and taxonomic local databases
by
GenoMax
141k
> I ask this as some BLAST command fields as scinames or sblastnames do not give any output with a classic nt BLAST If that information is…
Answer: BLAST using both nucleotides and taxonomic local databases
by
5heikki
11k
This has been discussed [many times][1] [1]: https://www.biostars.org/p/76551/
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by
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I think when you give indent to seuObj : Idents(seuObj) <- 'RNA_snn_res.0.1' You may wrongly assign other value to it such as …
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by
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In fact, there is no gold standard for cell type annotation. To achieve correct cell type classification, you can combine the two methos. F…
Answer: ScRNA data question
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In violin plot, a dot represents a cell. Actually, the straight lines you see in your infected image just means these cells have the same e…
Comment: Sequence read length shorter than flow cell specification
by
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141k
> the have sent data with different sequencing read lengths: 55bp pair ended and 80bp single ended If they sent data that is not what you…
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I have some off-the-chart dN/dS values for few genes (>20) when using your script on VCF obtained from a 20K plasmodium genomes (pf7K). | …
Answer: Sequence read length shorter than flow cell specification
by
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82k
It is the amount of reagent in the kit that determines read length. Sometimes index cycle reagents are allocated to R1/R2 or they used anot…
Comment: Why gatk VariantAnnotator required bam and coverage files
by
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161k
you don't need the bam file https://gatk.broadinstitute.org/hc/en-us/articles/13832654601755-VariantAnnotator : VariantAnnotator …
Comment: GAPIT p-value significance threshold
by
ginellegrenier
• 0
Hi, I was wondering if you have found a solution to this? Thanks!
Comment: PCA plot
by
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▴ 170
cross posted in bioconductor. [https://support.bioconductor.org/p/9157968/][1] [1]: https://support.bioconductor.org/p/9157968/
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by
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★ 2.3k
Which normalization method did you use for your data? I am guessing you had used SCTransform normalization for your data. Can you plot usin…
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by
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• 0
Hi Dan, I was wondering if you found out how to make the same graph with NFR and NBR regions with different curves. I was able to recreate…
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