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746 results • Page
4 of 15
Sort: replies
Rank
Views
Votes
Replies
1
vote
5
replies
299
views
Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 19 hours ago by
dthorbur
★ 2.0k • written 1 day ago by
BATMAN
• 0
5
votes
5
replies
320
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
10 days ago by
Chris
▴ 280
1
vote
5
replies
504
views
DYH17 Structure Prediction
BLAST
Protein-Structure-Prediction
24 days ago by
anasjamshed
▴ 120
0
votes
5
replies
443
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 23 days ago by
GenoMax
142k • written 23 days ago by
Bertalan_Takacs
▴ 90
1
vote
5
replies
218
views
Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
circos
atacseq
updated 2 days ago by
Pierre Lindenbaum
161k • written 2 days ago by
biology_inform
▴ 50
3
votes
5
replies
345
views
Generating mpileup file using samtools
mpileup
samtools
updated 15 days ago by
Joe
21k • written 15 days ago by
Ruqaiya
• 0
0
votes
5
replies
431
views
Telescope issue
Telescope
RNA-seq
updated 16 days ago by
GenoMax
142k • written 17 days ago by
eleven11
• 0
3
votes
5
replies
641
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
26 days ago by
n_navy
• 0
5
votes
5
replies
669
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 14 days ago by
Mbofire
• 0 • written 23 days ago by
Ming Tommy Tang
★ 3.9k
0
votes
5
replies
285
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 2 days ago by
GenoMax
142k • written 3 days ago by
chrisk
• 0
2
votes
5
replies
543
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
19 days ago by
ashaneev07
▴ 20
1
vote
5
replies
800
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
2
votes
4
replies
277
views
Where to get the following bed file?
WES
bed
reference
file
updated 11 days ago by
GenoMax
142k • written 11 days ago by
wyuan37
• 0
1
vote
4
replies
282
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 1 hour ago by
Joe
21k • written 9 days ago by
cput
• 0
2
votes
4
replies
1.4k
views
How to fix Error in dat[, batch == batch_level] : (subscript) logical subscript too long when removing batch effects
microarray
combat
batch-effect
median-normalization
updated 29 days ago by
Ram
43k • written 18 months ago by
Dominique
• 0
0
votes
4
replies
340
views
Perfom a Gene Ontology Analysis from GO terms txt file
RNA-Seq
GO
updated 18 days ago by
Ram
43k • written 18 days ago by
Hamtaro
▴ 50
0
votes
4
replies
407
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
5 days ago by
beginner123
• 0
1
vote
4
replies
487
views
GTF file for Rhinolophus sinicus
Rhinolophus-sinicus
GTF
updated 24 days ago by
atowns21
• 0 • written 6 months ago by
ara
• 0
2
votes
4
replies
229
views
Help with IGV abbreviation
igv
updated 3 days ago by
Ram
43k • written 4 days ago by
GeneC
• 0
3
votes
4
replies
287
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
patch
freeze
genome
updated 21 hours ago by
Jeremy Leipzig
22k • written 2 days ago by
Ali
• 0
0
votes
4
replies
255
views
How to handle duplicated genes in TCGA data?
TCGA
GDC
mRNA
updated 3 hours ago by
txema.heredia
▴ 130 • written 1 day ago by
Ngrin
• 0
0
votes
4
replies
664
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
29 days ago by
Kai Xin
• 0
3
votes
4
replies
369
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
masspec
uORF
peptide
updated 1 day ago by
GenoMax
142k • written 2 days ago by
Pierre Lindenbaum
161k
3
votes
4
replies
3.5k
views
any recommended tools for batch effect and normalization not written in R?
R
RNA-Seq
combat
python
batch-effect
updated 29 days ago by
Ram
43k • written 7.2 years ago by
dyollluap
▴ 310
2
votes
4
replies
395
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
updated 24 days ago by
swbarnes2
14k • written 25 days ago by
dxj294
• 0
3
votes
4
replies
322
views
Truncated metadata file report from ENA Portal API
ena
python
7 days ago by
Giulia
• 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 4 days ago by
Thind amarinder
▴ 340 • written 5.0 years ago by
garbuzov
▴ 70
3
votes
4
replies
423
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
22 days ago by
QX
• 0
0
votes
4
replies
623
views
how to find genes that are significantly expressed in brain cortex samples
rna-seq
gene-expression
updated 27 days ago by
ATpoint
82k • written 28 days ago by
rheab1230
▴ 140
2
votes
4
replies
720
views
Count all variants from vcf file
variants
vcf
Count
updated 11 days ago by
Pierre Lindenbaum
161k • written 21 months ago by
t.ali
• 0
2
votes
4
replies
298
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
3 days ago by
Esraa
• 0
1
vote
4
replies
3.2k
views
remove batch effect for multiple tumor data
RNA-Seq
batch-effect
updated 29 days ago by
Ram
43k • written 7.2 years ago by
hellocita
▴ 40
0
votes
4
replies
2.3k
views
MGLTools does not work in windows 11
windows-11
Autodock
windows
MGLTools
updated 3 days ago by
Ram
43k • written 13 months ago by
mohyeddine.taleb
• 0
3
votes
4
replies
474
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
updated 11 days ago by
Gordon Smyth
★ 7.2k • written 14 days ago by
SHN
▴ 40
0
votes
4
replies
241
views
Sequencing Depth (Read Depth) Calculations
depth
2 days ago by
LucisTheFather
• 0
0
votes
4
replies
309
views
Correlation Analysis
statistics
methylation
NGS
expression
7 days ago by
Researcher
▴ 30
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 10 days ago by
chloek88
• 0 • written 5.6 years ago by
Philipp Bayer
8.5k
1
vote
4
replies
417
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 7 days ago by
GenoMax
142k • written 4 weeks ago by
aniigodwinn
• 0
2
votes
4
replies
2.5k
views
How could I generate a gi_taxid_nucl.dmp file similar to the one previously hosted by NCBI?
ncbi
metagenomics
centrifuge
gi_taxid_nucl.dmp
taxonomy
updated 23 days ago by
ZhangYuanfeng
• 0 • written 2.5 years ago by
Frazier Baker
• 0
6
votes
4
replies
13k
views
Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode
trimmomatic
paired-end
updated 7 days ago by
Ruqaiya
• 0 • written 6.5 years ago by
dllopezr
▴ 130
1
vote
4
replies
776
views
What happened to Tombo Re-squiggle
Tombo
resquiggle
ONT
updated 29 days ago by
Ram
43k • written 4 months ago by
turcoa1
• 0
0
votes
4
replies
258
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
4 hours ago by
mavy
▴ 10
1
vote
4
replies
347
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 3 days ago by
Juke34
8.6k • written 5 days ago by
Vijith
▴ 30
1
vote
4
replies
502
views
cellranger error message
multiplexing
cellranger
updated 7 days ago by
Max
• 0 • written 3 months ago by
Alivia
▴ 10
1
vote
4
replies
284
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
2 days ago by
Arton
▴ 10
0
votes
4
replies
262
views
Galaxy StringTie error
stringtie
galaxy
4 days ago by
trkfs
• 0
1
vote
4
replies
1.7k
views
Batch correction and DE analysis of miRNA Seq data
miRNAseq
Differential-Expression
batch-effect
updated 29 days ago by
Ram
43k • written 5.1 years ago by
georgians
▴ 50
6
votes
4
replies
294
views
Details on salmon index
Salmon
updated 23 hours ago by
Rob
6.6k • written 2 days ago by
Lorenzo
• 0
0
votes
4
replies
282
views
How to extract cells of different species after mapping with combined genome?
snRNA-seq
scRNA-seq
updated 1 day ago by
Tony
• 0 • written 2 days ago by
vk
▴ 10
0
votes
4
replies
278
views
Merge clusters in Seurat UMAP
seurat
umap
1 day ago by
kilcdincer
▴ 10
746 results • Page
4 of 15
Recent Votes
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
Answer: ChatGPT optimized for bioinformatics questions
Comment: ChatGPT optimized for bioinformatics questions
C: How can I perform Differential expression analysis with just one control and one
C: How can I perform Differential expression analysis with just one control and one
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Recent Replies
Comment: calculating genomic coverage/ base overlap in R
by
1769mkc
★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks
by
ATpoint
82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner
by
Joe
21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression?
by
Gordon Smyth
★ 7.2k
See the exploration of isoform precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167. Our resul…
Comment: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF)
by
aidangcruickshank
▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data?
by
Ngrin
• 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2
by
swbarnes2
14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot
by
LauferVA
4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Answer: GG Sankey plot
by
bk11
★ 2.5k
You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
Answer: Trimming tool
by
ntsopoul
▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
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