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189 results • Page
2 of 4
Sort: replies
Rank
Views
Votes
Replies
0
votes
4
replies
269
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
10 hours ago by
Bibi
• 0
2
votes
4
replies
237
views
Help with IGV abbreviation
igv
updated 5 days ago by
Ram
43k • written 6 days ago by
GeneC
• 0
0
votes
4
replies
2.3k
views
MGLTools does not work in windows 11
windows-11
Autodock
windows
MGLTools
updated 5 days ago by
Ram
43k • written 13 months ago by
mohyeddine.taleb
• 0
1
vote
4
replies
356
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 5 days ago by
Juke34
8.6k • written 6 days ago by
Vijith
▴ 30
0
votes
4
replies
331
views
How to extract cells of different species after mapping with combined genome?
snRNA-seq
scRNA-seq
updated 3 days ago by
Tony
• 0 • written 4 days ago by
vk
▴ 10
2
votes
4
replies
310
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
5 days ago by
Esraa
• 0
2
votes
4
replies
5.6k
views
44% Successfully Assigned Fragments with featureCounts after 85% uniquely mapped reads with STAR
rna-seq
alignment
RNA-Seq
featureCounts
STAR
updated 6 days ago by
Thind amarinder
▴ 340 • written 5.0 years ago by
garbuzov
▴ 70
0
votes
3
replies
359
views
Snakemake wrapper issue
fastqc
snakemake
updated 6 days ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
0
votes
3
replies
29
views
Why most genes have high padj values
deg
padj
bulkRNA
updated 16 minutes ago by
ATpoint
82k • written 49 minutes ago by
mnx0723
• 0
3
votes
3
replies
250
views
getting exon coordinates
genomics
updated 3 days ago by
Ram
43k • written 3 days ago by
Xbox_27
• 0
1
vote
3
replies
209
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
updated 4 days ago by
Zhenyu Zhang
★ 1.2k • written 4 days ago by
shpak.max
▴ 50
0
votes
3
replies
280
views
Sam file Header problem
Sam
Header
problem
file
updated 3 days ago by
Pierre Lindenbaum
161k • written 4 days ago by
saifulislam99121
• 0
1
vote
3
replies
295
views
Using ggplotly in R
ggplot
ggplotly
updated 4 days ago by
jared.andrews07
★ 16k • written 5 days ago by
jen
▴ 10
3
votes
3
replies
368
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 6 days ago by
Mathew
▴ 140 • written 9 days ago by
Christopher
• 0
3
votes
3
replies
296
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 6 days ago by
Ram
43k • written 20 days ago by
Adyasha
• 0
0
votes
3
replies
200
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat
single-cell
scRNA-seq
R
updated 6 days ago by
Ram
43k • written 6 days ago by
yau
• 0
2
votes
3
replies
294
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio
Cibersort
R
6 days ago by
Azra
▴ 10
1
vote
3
replies
803
views
About runing Pilon on individual chromosomes when polish draft genome assembly
Pilon
chromosome
polish
genome
draft
updated 3 days ago by
sansan_96
▴ 90 • written 2.7 years ago by
boymin2020
▴ 80
1
vote
3
replies
283
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 3 days ago by
GenoMax
142k • written 6 days ago by
ohtang7
▴ 40
2
votes
3
replies
254
views
ggrepel function: geom_text_repel()
ggplot2
ggrepel
R
updated 3 days ago by
Ram
43k • written 4 days ago by
sooni
▴ 20
1
vote
3
replies
285
views
Tool:
Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes
Decimal
offtopic
Degrees
python
updated 3 days ago by
Ram
43k • written 4 days ago by
kuttibiotech2009
▴ 30
0
votes
3
replies
374
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
6 days ago by
mropri
▴ 150
1
vote
3
replies
451
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
6 days ago by
kalavattam
▴ 190
0
votes
3
replies
221
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 5 days ago by
GenoMax
142k • written 6 days ago by
RNAseqer
▴ 270
2
votes
3
replies
289
views
Finding variants within a subset of a BAM file
variant
calling
5 days ago by
ramiro.barrantes
• 0
0
votes
3
replies
211
views
How to access GWAVA software of data
GWAVA
updated 5 days ago by
GenoMax
142k • written 5 days ago by
nonaddldy
▴ 10
3
votes
3
replies
234
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
updated 3 days ago by
ATpoint
82k • written 4 days ago by
Alexandra
• 0
0
votes
3
replies
270
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 5 days ago by
noodle
▴ 580 • written 5 days ago by
doramora
▴ 10
0
votes
3
replies
172
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
4 days ago by
Esraa
• 0
2
votes
3
replies
219
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC
RNA-Seq
updated 5 days ago by
Ram
43k • written 5 days ago by
Prawesh
• 0
0
votes
3
replies
239
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
updated 2 hours ago by
nd48
▴ 20 • written 2 days ago by
Umer
▴ 50
2
votes
2
replies
274
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 3 days ago by
Ram
43k • written 3 days ago by
txema.heredia
▴ 130
0
votes
2
replies
219
views
Output file of samtools flagstat empty
samtools-flagstat
updated 6 days ago by
colindaven
6.4k • written 7 days ago by
ramendra.sarma
• 0
3
votes
2
replies
204
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 6 days ago by
ATpoint
82k • written 6 days ago by
jennyp0706
• 0
1
vote
2
replies
370
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
ComBat-seq
limma
RNA-seq
removeBatchEffect
batch-effect
updated 6 days ago by
Ram
43k • written 7 days ago by
t.fortunato.asquini
• 0
4
votes
2
replies
196
views
Duplicated sequence samtools
bowtie2
samtools
updated 6 days ago by
GenoMax
142k • written 6 days ago by
Moinuddin
• 0
0
votes
2
replies
441
views
News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
6 days ago by
David Langenberger
11k
1
vote
2
replies
1.3k
views
Extracting named fasta sequences according to list with Biopython
Biopython
FASTA
updated 6 days ago by
Rubayetul
• 0 • written 2.6 years ago by
lachiemck
• 0
3
votes
2
replies
289
views
imputation through beagle
panel
beagle
reference
imputation
6 days ago by
analyst
▴ 50
0
votes
2
replies
188
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
5 days ago by
IdaHao0921
• 0
1
vote
2
replies
270
views
How to interpret infinite odds ratio?
statistics
5 days ago by
Lukas
• 0
2
votes
2
replies
208
views
Genome Visualization Tools
bacterial
genome
updated 5 days ago by
GenoMax
142k • written 5 days ago by
dlera.lozano
▴ 10
1
vote
2
replies
213
views
Alphafold 3 pLDDT coloring scheme in chimerax?
ChimeraX
Alphaphold
Alphaphold3
updated 5 days ago by
colindaven
6.4k • written 5 days ago by
mbrav005
• 0
0
votes
2
replies
195
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
5 days ago by
melissa.joubert
• 0
2
votes
2
replies
206
views
genome finishing
finishing
genome
updated 4 days ago by
nd48
▴ 20 • written 4 days ago by
trezini
• 0
1
vote
2
replies
235
views
Doubt about the process of annotation, detection, identification and classification of transposable elements
annotation
TransposableElements
4 days ago by
MarcosCosta
• 0
0
votes
2
replies
232
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
4 days ago by
Chen
• 0
2
votes
2
replies
193
views
Cannot install bwa-mem2 via conda
conda
mamba
python
updated 3 days ago by
Ram
43k • written 4 days ago by
jsmith120f
• 0
1
vote
2
replies
234
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
3 days ago by
bioinfo
▴ 150
0
votes
2
replies
242
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 3 days ago by
Pierre Lindenbaum
161k • written 3 days ago by
melissachua90
▴ 70
189 results • Page
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Recent Votes
Answer: How to find tandem duplications pattern in a DNA sequence
A: How To Split One Big Sequence File Into Multiple Files With Less Than 1000 Seque
C: Snakemake vs. Nextflow: strengths and weaknesses
Answer: workflow management system : WDL, CWL, Ruffus, SnakeMake, etc
Sequence alignment on split read event such as inversion, duplication and complex nested events.
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
Comment: Add stats to the plot
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Recent Replies
Comment: Why most genes have high padj values
by
ATpoint
82k
788 differential genes is a lot. What is the problem?
Comment: Why most genes have high padj values
by
mnx0723
• 0
Sorry, I made edits.
Comment: Why most genes have high padj values
by
Pierre Lindenbaum
161k
Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the cod…
Comment: GO analysis: p-value range
by
marco.barr
▴ 130
Try adding: `scale_y_continuous(breaks=seq(0, max_count, by=0.05))`
Comment: Functional enrichment analysis for unique gene IDs
by
ATpoint
82k
If these genes do not have a symbol then it is utterly unlikely that anyone has looked at their function. I would get their Ensembl IDs and…
Comment: Add stats to the plot
by
marco.barr
▴ 130
The error is likely due to the fact that the structure of your data in data4.ts and data2.ts may not contain the Condition values. The grou…
Comment: How to find identical sequences in genome fasta file (by Python or any possible
by
Pierre Lindenbaum
161k
+ https://www.biostars.org/p/3003/ + https://www.biostars.org/p/9550118/ + https://www.biostars.org/p/158148/
Answer: How to find tandem duplications pattern in a DNA sequence
by
micah
▴ 30
I built a web application can directly find repeat unit and repeat times, try it at http://64.64.240.35:8050/. ![Dot plot][1] ![5 tandem …
Comment: What marks a De-Novo Genome assembly as FAILED?
by
nd48
▴ 20
I would urge you to consider different approaches for benchmarking before deciding on one. In particular, I found that assembling long read…
Comment: BiomartException: Query ERROR for existing dataset in BioMart
by
Luqman
• 0
I am using *pybiomart* which has Server inplace of BiomartServer, I used that as per above but still getting the same error. Also, when I a…
Comment: Blastn, need help to increase speed
by
m13113153781
• 0
mmseq2 is indeed a good acceleration solution, but its index files require ~ 6 T space....
Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
by
KHURRAM SHAHZAD
• 0
Thank you it works
Answer: Add stats to the plot
by
Ghada
• 0
I think this is what caused the error. we do not have group 1 and 2 in the statistical test results???? ![enter image description here][…
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
Bibi
• 0
@atpoint thanks you for your timely response. Can someone else shed light if we can compare the trend of DEGs using the scRNA and Bulk RNA…
Comment: Add stats to the plot
by
GenoMax
142k
Please use `101010` to format `code` so it is represented in monospace font. I have done this for you now.
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