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319 results • Page
2 of 7
Sort: Views
Rank
Views
Votes
Replies
1
vote
6
replies
375
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
4 days ago by
Umer
▴ 50
0
votes
4
replies
375
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
1 day ago by
mavy
▴ 10
0
votes
3
replies
372
views
Snakemake wrapper issue
fastqc
snakemake
updated 11 days ago by
Wei-Chen Pan
• 0 • written 10 weeks ago by
Matvii Mykhailichenko
• 0
3
votes
5
replies
370
views
Generating mpileup file using samtools
mpileup
samtools
updated 22 days ago by
Joe
21k • written 22 days ago by
Ruqaiya
• 0
1
vote
4
replies
368
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 10 days ago by
Juke34
8.6k • written 12 days ago by
Vijith
▴ 30
5
votes
5
replies
367
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
17 days ago by
Chris
▴ 280
3
votes
4
replies
362
views
Truncated metadata file report from ENA Portal API
ena
python
14 days ago by
Giulia
• 0
0
votes
5
replies
361
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
12 days ago by
SilhouetteQ
• 0
1
vote
4
replies
359
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 7 days ago by
Joe
21k • written 16 days ago by
cput
• 0
1
vote
3
replies
357
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
20 days ago by
Lada
▴ 30
1
vote
3
replies
357
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 24 days ago by
GenoMax
142k • written 25 days ago by
jeffrey.maurer.informatics
• 0
2
votes
3
replies
356
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 22 days ago by
dthorbur
★ 2.0k • written 22 days ago by
Vijith
▴ 30
0
votes
4
replies
355
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
5 days ago by
Bibi
• 0
0
votes
0
replies
351
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
22 days ago by
NorbertK
▴ 10
0
votes
3
replies
348
views
KEGG Pathways
r
RNA-seq
updated 25 days ago by
Ram
44k • written 25 days ago by
Sudip
• 0
1
vote
2
replies
342
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
24 days ago by
Nafi
• 0
0
votes
3
replies
342
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 25 days ago by
GenoMax
142k • written 25 days ago by
kim
• 0
0
votes
4
replies
341
views
Correlation Analysis
statistics
methylation
NGS
expression
14 days ago by
Researcher
▴ 30
0
votes
4
replies
336
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
3 days ago by
Luqman
• 0
3
votes
3
replies
332
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 14 days ago by
Ram
44k • written 15 days ago by
Omics data mining
▴ 260
0
votes
1
reply
331
views
LDhat lookup table
LDhat
updated 1 day ago by
Ram
44k • written 11 months ago by
Matteo
▴ 10
0
votes
4
replies
331
views
Genbank File Format
gbkformat
25 days ago by
alenew.am
• 0
0
votes
1
reply
330
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 18 days ago by
andres.firrincieli
3.6k • written 19 days ago by
Antonio
• 0
0
votes
2
replies
329
views
Annovar using R package
Annovar
gnomAD
R
29 days ago by
DKA
▴ 40
0
votes
5
replies
326
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
updated 17 days ago by
Joe
21k • written 17 days ago by
Lemonhope
• 0
0
votes
2
replies
325
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 12 days ago by
Zhenyu Zhang
★ 1.2k • written 22 days ago by
yahn
• 0
0
votes
5
replies
317
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 9 days ago by
GenoMax
142k • written 10 days ago by
chrisk
• 0
0
votes
2
replies
315
views
How are score_weights calculated in this code?
single-cell
14 days ago by
carolofharvest
▴ 40
1
vote
3
replies
310
views
Odd alignment question/finding
Alignment
updated 22 days ago by
barslmn
★ 2.2k • written 23 days ago by
poordumbsillyidiot
• 0
1
vote
2
replies
309
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
23 days ago by
rianna.collins
• 0
3
votes
3
replies
308
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 11 days ago by
Ram
44k • written 25 days ago by
Adyasha
• 0
0
votes
2
replies
307
views
Traveler with Infernal mapping failed
r2dt
updated 6 days ago by
anton.i.petrov
• 0 • written 3 months ago by
Larissa
• 0
0
votes
3
replies
305
views
Sam file Header problem
Sam
Header
problem
file
updated 8 days ago by
Pierre Lindenbaum
162k • written 9 days ago by
saifulislam99121
• 0
0
votes
3
replies
301
views
What is a good way to do gene differentials in single cell data where one group is small 90 cells and the other group 30,000 cells or 2000 cells.
cell
RNA-Seq
single
updated 1 day ago by
ATpoint
82k • written 1 day ago by
shahzaibali
• 0
0
votes
2
replies
301
views
Downloading older version of a tool
Alignment
tools
21 days ago by
Ruqaiya
• 0
0
votes
1
reply
300
views
creating batch colum for batch correction
batch-correction
combat
19 days ago by
Expert
▴ 10
0
votes
2
replies
297
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 14 days ago by
GenoMax
142k • written 21 days ago by
Ximena
• 0
1
vote
2
replies
293
views
Downloading full alignments from Pfam
pfam
20 days ago by
bef1
• 0
1
vote
3
replies
290
views
STAR aligner error
RNA-seq
STAR
slurm
updated 16 days ago by
Ram
44k • written 17 days ago by
M.
▴ 30
0
votes
0
replies
287
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
26 days ago by
SSSJec
• 0
0
votes
2
replies
286
views
Help with generating annotation database for dog genome to use in ANNOVAR for variant annotation of dog tumor sequences
ANNOVAR
17 days ago by
sainavyav22
• 0
0
votes
1
reply
286
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort.
SAMtools.
BAM.
SAM.
updated 18 days ago by
GenoMax
142k • written 18 days ago by
Sony
▴ 10
0
votes
2
replies
283
views
How can I calculate the OS of each patient?
overall-survival
4 days ago by
Pedro
• 0
1
vote
1
reply
279
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 29 days ago by
ATpoint
82k • written 29 days ago by
AaronJaime
• 0
0
votes
1
reply
278
views
Subsetting and merging back Seurat Object brings different results
Seurat
23 days ago by
Bine
▴ 60
0
votes
4
replies
277
views
Galaxy StringTie error
stringtie
galaxy
11 days ago by
trkfs
• 0
0
votes
2
replies
277
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
18 days ago by
Ahiad Chen Zion
• 0
0
votes
2
replies
276
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 8 days ago by
Pierre Lindenbaum
162k • written 8 days ago by
melissachua90
▴ 70
0
votes
3
replies
273
views
Software to separate reads from different individuals
software
development
nanopore
updated 25 days ago by
GenoMax
142k • written 26 days ago by
njornet
▴ 20
1
vote
1
reply
271
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 24 days ago by
Ram
44k • written 25 days ago by
Jonathan Yoou
▴ 60
319 results • Page
2 of 7
Recent Votes
A: Looking for differential gene expression between treatment, within a specific cl
How to compare cell-type ratios in sc-RNA seq data?
How to calculate cell type frequency between two groups in single cell data
DESeq2 single cell pseudobulk
Comment: Number of non-ATCG nucleotides replaced by Salmon
Answer: Number of non-ATCG nucleotides replaced by Salmon
Answer: Error when i use EVidenceModeler to do the genome annotation
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Recent Replies
Comment: Harmony integration group.by.var parameter
by
Picasa
▴ 640
For downstream analysis, after integration, my plan is to annotate each cluster/cell type and then perform a DGE analysis of KO versus WT f…
Comment: How to calculate cell type frequency between two groups in single cell data
by
Bastien Hervé
5.3k
That is correct
Answer: Setting a threshold on gene expression for subsetting (scRNA-seq)
by
ATpoint
82k
That depends on the data and the marker. Generally I would plot violins per cluster for the marker(s) and see whether one robustly overexpr…
Comment: Error when i use EVidenceModeler to do the genome annotation
by
peanut
• 0
thank you so much ,i get it
Comment: Number of non-ATCG nucleotides replaced by Salmon
by
Tonya S.
▴ 10
Oops, yes, that must be where they are coming from. For some reason, I was thinking the genome was just soft-masked. How embarrassing! Than…
Answer: Number of non-ATCG nucleotides replaced by Salmon
by
Rob
6.6k
If there are no other signs that anything is awry, I probably wouldn't worry about this. Is it possible that these non-canonical nucleotid…
Comment: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvage
by
Brian Bushnell
20k
I examined nine 10B runs and five 25B runs (we just started getting 25B flowcells a few months ago). I did not pay close attention but it …
Comment: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvage
by
GenoMax
142k
> I don't know how widespread these issues are outside of JGI. Very few small/medium sequencing centers likely have NovaSeq X. This is the…
Comment: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvage
by
Brian Bushnell
20k
Supporting figures, taken from some slides I prepared for internal use. HDist 0, 1, and 2 correspond to 0, 1, and 2 mismatches allowed in …
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
This works. Thank you so so much!
Comment: Harmony integration group.by.var parameter
by
jared.andrews07
★ 17k
>I am not sure, but using "Sample_ID" might remove the differences between the conditions right ? More than likely, it'd at least impact t…
Comment: Harmony integration group.by.var parameter
by
Picasa
▴ 640
Thanks jared.andrews07 for your answer. So, you are suggesting to use only "Donor" in the integration? ```r RunHarmony(seu_obj, group.by.…
Comment: Single cell analysis: Unable to subset cells in seurat object using desired nFea
by
sc_analysis
• 0
I am not sure what should be the cut off. Looking at the vlnplot before subsetting i thought most of the cells are falling under 7500 nfeat…
Comment: How to calculate cell type frequency between two groups in single cell data
by
Sara
▴ 30
Thank you for your comment and sorry if this question might be so basic. How can I normalize the number of cells? If I am not wrong the i…
Comment: Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
by
Deepthi
• 0
I unzipped the fastq files to check whether reads are trimmed adapter or not. I have checked the quality control using fastqc they are go…
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