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1,000 results • Page
1 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
14
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
52 minutes ago by
Aaliya
• 0
0
votes
0
replies
38
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
6 hours ago by
Kash
▴ 110
0
votes
1
reply
58
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 1 hour ago by
Mensur Dlakic
★ 27k • written 7 hours ago by
benguyarenbeyaz98
• 0
0
votes
1
reply
81
views
How to calculate identity percentage between proteins contained in a FASTA file?
percentage
FASTA
alignment
identity
updated 6 hours ago by
GenoMax
141k • written 8 hours ago by
v.berriosfarias
▴ 140
2
votes
9
replies
727
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 4 hours ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
10
replies
270
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
2 hours ago by
atowns21
• 0
0
votes
1
reply
86
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 9 hours ago by
bk11
★ 2.3k • written 10 hours ago by
alphaflylizard
• 0
0
votes
1
reply
73
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
updated 11 hours ago by
Pierre Lindenbaum
161k • written 12 hours ago by
Lada
▴ 30
0
votes
0
replies
52
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
13 hours ago by
ohtang7
▴ 40
0
votes
1
reply
97
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 16 hours ago by
GenoMax
141k • written 16 hours ago by
Srinka
▴ 20
0
votes
4
replies
186
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
updated 14 hours ago by
GenoMax
141k • written 16 hours ago by
njornet
▴ 20
0
votes
0
replies
58
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 14 hours ago by
Ram
43k • written 17 hours ago by
SHREYA
• 0
0
votes
0
replies
66
views
Merging replicates from Encode project
CHIP-seq
encode
17 hours ago by
Nurken
• 0
1
vote
3
replies
163
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
18 hours ago by
WouterDeCoster
47k
0
votes
3
replies
169
views
some error in building kraken2 database
metagenome
kraken2
3 hours ago by
Art1ess
• 0
0
votes
1
reply
100
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 14 hours ago by
bk11
★ 2.3k • written 19 hours ago by
Susmita Mandal
▴ 110
1
vote
1
reply
131
views
Failed kmer content
kmer
illumina
ngs
updated 14 hours ago by
Ram
43k • written 22 hours ago by
Kasturi
• 0
0
votes
2
replies
160
views
Heatmap and rna-seq
RNA-Seq
Heatmap
and
updated 7 hours ago by
Istvan Albert
100k • written 23 hours ago by
qudrat.nii
▴ 10
0
votes
0
replies
66
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 13 hours ago by
Ram
43k • written 1 day ago by
SSSJec
• 0
0
votes
1
reply
120
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 1 day ago by
Ram
43k • written 1 day ago by
Cameron.walker9900
• 0
0
votes
8
replies
256
views
Error in cnetplot enrichplot package
R
updated 1 day ago by
Ram
43k • written 1 day ago by
Farhad
• 0
0
votes
0
replies
95
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 1 day ago by
Ram
43k • written 1 day ago by
maxime.policarpo
▴ 200
0
votes
0
replies
80
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 1 day ago by
Ram
43k • written 1 day ago by
sansan_96
▴ 80
0
votes
0
replies
85
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 14 hours ago by
Ram
43k • written 1 day ago by
Amélie
• 0
0
votes
0
replies
131
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 1 day ago by
Ram
43k • written 1 day ago by
Oak
▴ 10
1
vote
3
replies
2.4k
views
Problem to remove subset of patients with plink
plink
PED
updated 1 day ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
1
vote
5
replies
223
views
Downsampling fastq file
downsample
fastq
updated 1 day ago by
Ram
43k • written 1 day ago by
marco.barr
▴ 80
0
votes
1
reply
116
views
tbtool
tbtool
updated 1 day ago by
Ram
43k • written 1 day ago by
Raman
• 0
0
votes
2
replies
168
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 1 day ago by
i.sudbery
19k • written 1 day ago by
Patadu94
• 0
0
votes
2
replies
138
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 1 day ago by
Mensur Dlakic
★ 27k • written 1 day ago by
emmanouil.a
▴ 120
0
votes
1
reply
110
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 1 day ago by
ATpoint
82k • written 1 day ago by
enanoide
• 0
0
votes
0
replies
76
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
1 day ago by
manaswwm
▴ 490
0
votes
0
replies
66
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
18 hours ago by
alifafiq1
• 0
0
votes
0
replies
76
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
1 day ago by
feather-W
• 0
2
votes
3
replies
187
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
updated 19 hours ago by
Pierre Lindenbaum
161k • written 1 day ago by
samuelkalandarov2002
▴ 10
0
votes
0
replies
72
views
Annotating single cell data automatically
cell
annotation
single
1 day ago by
Gerard
• 0
0
votes
1
reply
134
views
RNA-seq bacteria contamination
RNA-seq
updated 1 day ago by
GenoMax
141k • written 1 day ago by
sh
• 0
0
votes
0
replies
65
views
Imputation advice
imputation
1 day ago by
kl
▴ 10
0
votes
0
replies
80
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
1 day ago by
Enrique
• 0
0
votes
0
replies
68
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
1 day ago by
sativus
▴ 20
0
votes
0
replies
73
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
1 day ago by
Biostars2200
• 0
0
votes
0
replies
105
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 1 day ago by
Carlo Yague
8.7k • written 2 days ago by
Atul K.
• 0
2
votes
5
replies
412
views
Marking duplicates using UMIs
Deduplication
UMI
updated 1 day ago by
i.sudbery
19k • written 3 days ago by
Lipika
• 0
0
votes
0
replies
133
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 2 days ago by
Ram
43k • written 3 days ago by
sainavyav22
• 0
0
votes
0
replies
136
views
Bacterial genome alignment with mauve
Bacteria
mauve
genome
3 days ago by
rthapa
▴ 90
0
votes
0
replies
128
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation
CGenFF
Gromacs
VMD
3 days ago by
Mamatha Y S
• 0
0
votes
2
replies
242
views
bam merging for archaic samples
samtools
bam
updated 2 days ago by
Ram
43k • written 3 days ago by
Matteo Ungaro
▴ 100
1
vote
0
replies
531
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers
TRINITY
3 days ago by
mathavanbioinfo
▴ 90
0
votes
0
replies
205
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
3 days ago by
abhishekghadge
• 0
2
votes
5
replies
668
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 3 days ago by
Jesse
▴ 740 • written 4 days ago by
Ann
★ 2.4k
1,000 results • Page
1 of 20
Recent Votes
Comment: Per base sequence content error in RNAseq analysis
Answer: Gene set enrichment analysis differences between 2020 and 2024
Answer: Gene set enrichment analysis differences between 2020 and 2024
Answer: Gene set enrichment analysis differences between 2020 and 2024
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
Comment: TCGA2STAT Error: Firehose connection
Answer: HaplotypeCaller - only SNPs
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▴ 140
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AdviceSeeker
• 0
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★ 2.4k
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marco.barr
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141k
Recent Replies
Comment: How to compare the quality of assemblies
by
kirillkirilenko
▴ 40
A haploid assembly is our goal. For purging we used prefix.p_ctg.gfa (assembly graph of primary contigs).
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
by
Istvan Albert
100k
What I mean is that no sequencing run can be calibrated with the claimed precision. Where it could correctly distinguish between basecalls …
Comment: HaplotypeCaller - only SNPs
by
analyst
▴ 20
After HaplotypeCaller, you can use gatk SelectVariants to extract snps or indels from vcf file ([link to command][1]) [1]: https://gatk…
Comment: GTF file for Rhinolophus sinicus
by
atowns21
• 0
Ah gotcha. I guess what doesn't make sense to me is why a [paper][1] published in 2022 uses that reference genome. [1]: https://www.na…
Answer: Wilcox test using data slot (log normalized count values) of scRNA-seq between t
by
yxwucq
• 0
The best way is to generate a pseudo-bulk aggregation then apply edgeR or DESeq2. You can also directly use wilcoxon on sc-level, since man…
Comment: How to solve this RoseTTAFold colaboratory error?
by
Mensur Dlakic
★ 27k
There is a dedicated Discord group that deals with everything related to ColabFold and its derivatives. Below is an invitation to join that…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
by
atowns21
• 0
Hmm, okay I'm not sure what is going on, but here is what I did: 1. Downloaded a single fastq: `parallel-fastq-dump --tmpdir . --threads …
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
by
HyperEvo
• 0
Ok, thank you so much~
Comment: GTF file for Rhinolophus sinicus
by
GenoMax
141k
I was able to get the GTF file. I tried the fasta genome and it seemed to work but I did not complete the download. If you choose to ignore…
Comment: some error in building kraken2 database
by
Art1ess
• 0
I have 2 files output, no error logs... the .kreport file: 100.00 160136511 160136511 U 0 unclassified head .res…
Comment: TCGA2STAT Error: Firehose connection
by
LauferVA
4.2k
agree. from a data-centric (rather than software centric) standpoint, it shouldn't be hard to get the TCGA data you are looking for from o…
Comment: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
yep. in this case id definitely start with the grant numbers themselves as others have indicated. i did not recommend this before due to un…
Comment: GTF file for Rhinolophus sinicus
by
atowns21
• 0
This download doesn't seem to work for me. There is a message on the website saying "Warning: contaminated. Status: RefSeq GCF_001888835.1 …
Answer: HaplotypeCaller - only SNPs
by
Pierre Lindenbaum
161k
Filter the vcf dowstream after haplotypecaller using bcftools or gatk variantfiltration
Answer: Gene set enrichment analysis differences between 2020 and 2024
by
geneontologyhelp
▴ 380
We have releases about monthly in order to keep our data accurate and reflect current understanding. In 4 years, there have been about 40 r…
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