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314 results • Page
1 of 7
Sort: Votes
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Views
Votes
Replies
5
votes
7
replies
520
views
RNA seq analysis
DESeq
RNA-seq
4 days ago by
Jacek
▴ 20
5
votes
5
replies
349
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
12 days ago by
Chris
▴ 280
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq
RNA-Seq
exon
updated 13 days ago by
Sara
▴ 30 • written 6.7 years ago by
Lila M
★ 1.2k
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
20 days ago by
anna
▴ 20
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 17 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
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
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 11 days ago by
chloek88
• 0 • written 5.6 years ago by
Philipp Bayer
8.5k
3
votes
8
replies
638
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
13 days ago by
Qroid
▴ 40
3
votes
1
reply
209
views
Question about methylation location
Methylation
WGBS
bisulfide
updated 9 days ago by
dthorbur
★ 2.0k • written 10 days ago by
Eren
• 0
3
votes
4
replies
332
views
Truncated metadata file report from ENA Portal API
ena
python
9 days ago by
Giulia
• 0
3
votes
7
replies
423
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
20 days ago by
salias
• 0
3
votes
5
replies
353
views
Generating mpileup file using samtools
mpileup
samtools
updated 16 days ago by
Joe
21k • written 16 days ago by
Ruqaiya
• 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
2
votes
3
replies
337
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 16 days ago by
dthorbur
★ 2.0k • written 17 days ago by
Vijith
▴ 30
2
votes
2
replies
2.6k
views
Pindel Segmentation Fault Error
pindel
updated 15 days ago by
Ruqaiya
• 0 • written 10.3 years ago by
Yuelin
▴ 20
2
votes
9
replies
1.1k
views
HGVS Nomenclature of Multiple Indels found in Cis
Nomenclature
HGVS
17 hours ago by
LauferVA
4.2k
2
votes
5
replies
798
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 29 days ago by
Jesse
▴ 770 • written 4 weeks ago by
Ann
★ 2.4k
2
votes
2
replies
255
views
Raw counts using stringtie
stringtie
RNA-seq
updated 16 days ago by
GenoMax
142k • written 16 days ago by
ahmad.sajad4541
• 0
2
votes
9
replies
947
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 26 days ago by
LauferVA
4.2k • written 7 months ago by
Gnana
• 0
2
votes
4
replies
388
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
25 days ago by
samuelkalandarov2002
▴ 10
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
2
votes
2
replies
1.8k
views
Parametric or non-parametric tests for qPCR significance testing between treatments?
qPCR
statistical test
parametric
non-parametric
updated 16 days ago by
e.r.zakiev
▴ 210 • written 3.9 years ago by
n.anuragsharma
▴ 40
2
votes
3
replies
359
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 10 days ago by
bk11
★ 2.5k • written 15 days ago by
Yoosef
▴ 60
2
votes
2
replies
339
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 25 days ago by
Ram
43k • written 26 days ago by
v.berriosfarias
▴ 140
2
votes
5
replies
548
views
Marking duplicates using UMIs
Deduplication
UMI
updated 27 days ago by
i.sudbery
19k • written 29 days ago by
Lipika
• 0
2
votes
5
replies
958
views
Retrieval of Active site information programmatically
Catalytic
Python
Active
PDB
site
Site
updated 20 days ago by
Wayne
★ 2.0k • written 2.1 years ago by
arinjoy
• 0
2
votes
2
replies
249
views
PDB related issue
rcsb
pdb
updated 21 days ago by
noodle
▴ 580 • written 21 days ago by
Nafi
• 0
1
vote
2
replies
297
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
18 days ago by
rianna.collins
• 0
1
vote
1
reply
187
views
constructing pangenome through psvcp
psvcp
pangenome
1 day ago by
analyst
▴ 50
1
vote
2
replies
327
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
18 days ago by
Nafi
• 0
1
vote
1
reply
300
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 1 day ago by
nguyenn6
• 0 • written 3 months ago by
star
▴ 10
1
vote
2
replies
284
views
alignment result
RNA-seq
samtools
hisat2
25 days ago by
ahmad.sajad4541
• 0
1
vote
6
replies
2.8k
views
Segmentation fault using gemma
gemma
gwas
updated 20 days ago by
dimpleadiwal050896
• 0 • written 5.0 years ago by
ggman
▴ 90
1
vote
3
replies
344
views
some error in building kraken2 database
metagenome
kraken2
26 days ago by
Art1ess
• 0
1
vote
4
replies
508
views
cellranger error message
multiplexing
cellranger
updated 9 days ago by
Max
• 0 • written 3 months ago by
Alivia
▴ 10
1
vote
0
replies
145
views
What is Deepvariant default filtering values ?
vcf
calling
filter
variant
deepvariant
10 days ago by
Shae
▴ 10
1
vote
0
replies
176
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
24 days ago by
KABILAN
▴ 70
1
vote
2
replies
284
views
permutation test in edgeR
rna-seq
edgeR
updated 28 days ago by
Gordon Smyth
★ 7.2k • written 6 weeks ago by
Netanel
• 0
1
vote
2
replies
260
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 19 days ago by
Ram
43k • written 20 days ago by
Ravita
• 0
1
vote
4
replies
331
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 1 day ago by
Joe
21k • written 11 days ago by
cput
• 0
1
vote
3
replies
385
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 21 days ago by
ATpoint
82k • written 22 days ago by
Francesco
▴ 10
1
vote
1
reply
190
views
student
epitranscriptomics
updated 12 days ago by
ATpoint
82k • written 12 days ago by
useriwa
• 0
1
vote
0
replies
179
views
phasing tumor long-reads
nanopore
ONT
haplotag
phasing
tumor
10 days ago by
eebloom
▴ 80
1
vote
8
replies
563
views
Downsampling fastq file
downsample
fastq
19 days ago by
marco.barr
▴ 130
1
vote
0
replies
197
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
24 days ago by
rohitsatyam102
▴ 870
1
vote
6
replies
418
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 16 days ago by
GenoMax
142k • written 4 weeks ago by
eebloom
▴ 80
1
vote
3
replies
456
views
PCA plot
DESeq2
PCAplot
updated 21 days ago by
LauferVA
4.2k • written 25 days ago by
Aaliya
▴ 10
1
vote
16
replies
751
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
updated 1 day ago by
GenoMax
142k • written 4 days ago by
hophuquy0944
• 0
1
vote
2
replies
212
views
Repeated testing/data mining in RNA Seq
repeated
RNA-Seq
mining
testing
data
12 days ago by
robert.flynn.21
• 0
1
vote
2
replies
288
views
Downloading full alignments from Pfam
pfam
14 days ago by
bef1
• 0
314 results • Page
1 of 7
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
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.
Answer: is there a tool to recover corrupted fastq files
by
Tommaso
• 0
You may also want to give a try to **FastqWiper** (https://github.com/mazzalab/fastqwiper)
Comment: Add stats to the plot
by
Ghada
• 0
Thanks. That helpful. I am getting this error data4_test <- data4.ts%>% ungroup() %>% t.test(data =.,value ~ Condition)%>% + …
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