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181 results • Page
1 of 4
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0
votes
0
replies
34
views
Downloading full alignments from Pfam
pfam
3 hours ago by
bef1
• 0
0
votes
1
reply
665
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq
R
cellassign
batch-effect
updated 3 hours ago by
Francesco
▴ 10 • written 3.3 years ago by
gt
▴ 30
1
vote
1
reply
154
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 7 hours ago by
ATpoint
82k • written 1 day ago by
vanbelj
▴ 40
2
votes
6
replies
1.1k
views
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq
Salmon
Isoseq
updated 6 hours ago by
Ram
43k • written 8 months ago by
Calum
▴ 10
0
votes
0
replies
43
views
adjusting for confounders in LMER in R
confounders
LMER
R
8 hours ago by
rene.j.erhardt
▴ 20
0
votes
9
replies
178
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
updated just now by
GenoMax
141k • written 12 hours ago by
Ruqaiya
• 0
1
vote
2
replies
133
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 32 minutes ago by
Ram
43k • written 17 hours ago by
Francesco
▴ 10
0
votes
0
replies
72
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
17 hours ago by
tnminh89
▴ 10
8
votes
8
replies
616
views
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 2 hours ago by
Philipp Bayer
8.3k • written 20 hours ago by
noodle
▴ 530
0
votes
0
replies
80
views
Extract protein sequence
fasta
alighment
blast
19 hours ago by
anna
▴ 20
0
votes
0
replies
75
views
Filter low express genes in microarray data
microarray
19 hours ago by
Chris
▴ 260
0
votes
1
reply
262
views
absolute path for symbolic links in Snakefile
Snakemake
updated 20 hours ago by
Jesse
▴ 740 • written 8 days ago by
yifangt86
▴ 60
0
votes
2
replies
274
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 20 hours ago by
Jesse
▴ 740 • written 3 days ago by
Broccoli
• 0
2
votes
3
replies
256
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 21 hours ago by
Arup Ghosh
3.2k • written 1 day ago by
chaco001
▴ 40
1
vote
3
replies
274
views
Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:1.1.1.4, 1.1.1.-, 1.1.1.303)?
ontology
metagenomics
database
enzymes
genomics
updated 14 hours ago by
Mensur Dlakic
★ 27k • written 1 day ago by
O.rka
▴ 710
0
votes
1
reply
162
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
updated 1 day ago by
Gordon Smyth
★ 7.0k • written 2 days ago by
hagl
▴ 10
0
votes
2
replies
195
views
Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
RNA-Seq
edgeR
1 day ago by
Guille
• 0
1
vote
1
reply
149
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
updated 1 day ago by
Gordon Smyth
★ 7.0k • written 1 day ago by
pairedttest
▴ 10
3
votes
6
replies
1.9k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 1 day ago by
Ram
43k • written 2.4 years ago by
SYOSY
▴ 10
0
votes
0
replies
373
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
1 day ago by
biocellbio
• 0
4
votes
8
replies
534
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 1 day ago by
Alex Reynolds
35k • written 2 days ago by
J
▴ 10
4
votes
7
replies
595
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 1 day ago by
dsull
★ 5.9k • written 5 days ago by
qudrat.nii
▴ 10
19
votes
11
replies
14k
views
10 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 2 days ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
2
votes
2
replies
262
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 2 days ago by
dsull
★ 5.9k • written 2 days ago by
Aaliya
▴ 10
3
votes
0
replies
152
views
News:
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy
Generative-AI
scRNA
Machine-Learning
updated 1 day ago by
Ram
43k • written 2 days ago by
Claire Watson
▴ 60
0
votes
2
replies
226
views
Rare Disease Variant Pathway Analysis
Pathway-analysis
updated 1 day ago by
Ram
43k • written 2 days ago by
The_PyPanda
▴ 10
0
votes
0
replies
158
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
2 days ago by
HarperReed
• 0
3
votes
3
replies
230
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 2 days ago by
GenoMax
141k • written 2 days ago by
sapuizait
▴ 10
1
vote
0
replies
120
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
2 days ago by
KABILAN
▴ 50
0
votes
0
replies
130
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 1 day ago by
Ram
43k • written 2 days ago by
SineWave
• 0
0
votes
0
replies
126
views
RNA-seq: full length gene
RNA-seq
updated 1 day ago by
Ram
43k • written 2 days ago by
Nargis
• 0
1
vote
7
replies
366
views
gvcf joint calling
WES
GATK
VCF
gVCF
6 hours ago by
zihanss
• 0
0
votes
0
replies
119
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
2 days ago by
turcoa1
• 0
3
votes
3
replies
252
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 2 days ago by
swbarnes2
14k • written 2 days ago by
M
• 0
0
votes
0
replies
130
views
Designing single-stable RNA molecules
structure
RNA
2 days ago by
Edna
• 0
0
votes
0
replies
145
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
2 days ago by
simplitia
▴ 130
0
votes
1
reply
179
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 2 days ago by
ATpoint
82k • written 2 days ago by
AaronJaime
• 0
0
votes
2
replies
242
views
BLAST using both nucleotides and taxonomic local databases
blast
ncbi
taxid
taxonomy
updated 2 days ago by
GenoMax
141k • written 3 days ago by
Begonia_pavonina
▴ 150
0
votes
2
replies
275
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
updated 2 days ago by
Ram
43k • written 3 days ago by
Assa Yeroslaviz
★ 1.8k
1
vote
2
replies
275
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
17 hours ago by
Francesco
▴ 10
1
vote
6
replies
378
views
ScRNA data question
scRNA
Vlnplot
Samples
1 day ago by
starswillfade
▴ 10
0
votes
0
replies
144
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
2 days ago by
avocado123
• 0
0
votes
0
replies
138
views
News:
Master Meta-analysis with R (May 13-16) - Online!
Meta-Analysis
Statistics
R
updated 2 days ago by
Ram
43k • written 2 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
136
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
2 days ago by
Emily
▴ 10
1
vote
0
replies
153
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
2 days ago by
rohitsatyam102
▴ 850
0
votes
0
replies
138
views
how to read graph_test output of monocle 3
monocle3
2 days ago by
synat.keam
▴ 100
0
votes
0
replies
170
views
Job:
CTO/founding engineer role at Voyant Bio
engineer
2 days ago by
Assaf
• 0
0
votes
1
reply
468
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 3 days ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
3
votes
4
replies
309
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
2 days ago by
QX
• 0
2
votes
1
reply
219
views
Finding orthologs between genome error
OMA
OMAbrowser
updated 3 days ago by
Adrian Altenhoff
★ 1.1k • written 3 days ago by
hemantcnaik
• 0
181 results • Page
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How to input margin to UpsetR figure
Comment: How to assign cell types after integration in scRNA
NGS forensics: how to know if data is fabricated
Answer: ChIP-seq datasets: input samples omitted?
Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
A: Deeptools plotHeatmap - Maintain Order of Input BED file
Comment: NGS forensics: how to know if data is fabricated
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Recent Replies
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
Also, there is no mention of adapter sequence so which adapter sequence should i use to remove it from some other reads?
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
Also, Do you think i can reproduce at least most part of the data from the paper just on my laptop? It has 4 logical processors (Intel(R) C…
Comment: NGS forensics: how to know if data is fabricated
by
Philipp Bayer
8.3k
While I think this is an interesting case, I've before found cleaned 'raw' data on SRA. It happens: bioinformaticians receive the raw data,…
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
1. What does clipped Fastq mean? both forward and reverse reads in the same file? 2. Why would you remove 2000bp contigs? I feel it will gi…
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
Well, I downloaded both the reads from-[LINK][1]. Thats all i did. Thats the only thing i need to do, right? I'l try spades. [1]: http…
Comment: How to assign cell types after integration in scRNA
by
Francesco
▴ 10
Thanks for the fast reply.. however i had only partially understood the answer. Is correct saying that low-representation integration and b…
Answer: Can I run cellassign on samples independently if there is batch effect present?
by
Francesco
▴ 10
Hi! Whenever you do make independent analysis or aggregate data and analyze them, most cell type assignment tools start from raw counts to …
Comment: gvcf joint calling
by
zihanss
• 0
Thanks for your comment, I get it now.
Answer: ChIP-seq datasets: input samples omitted?
by
ATpoint
82k
In my hands (and from what I know based on many years here) inputs are almost exclusively used during peak calling to correct for loci-spec…
Comment: How to assign cell types after integration in scRNA
by
ATpoint
82k
No difference here. After all you typically want a label per cluster/group, so either subset to the control condition to do the assignment,…
Comment: Differential Expression using Isoseq-supplemented reference transcriptome
by
gaoanwei
• 0
I found the question and ASK the GPT4 turbo
Answer: Differential Expression using Isoseq-supplemented reference transcriptome
by
gaoanwei
• 0
Your approach seems reasonable and well-informed, though it's perhaps less customary in the field, which could be why you haven't found pap…
Answer: How many reads for WGS Sequencing?
by
Mensur Dlakic
★ 27k
It takes 29 seconds to assemble this genome (20 CPUs) with the following statistics: 135 contigs, total 2821177 bp, min 200 bp, max …
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 530
IMO (and unfortunately) there needs to be an effort to develop these algorithms.
Comment: gvcf joint calling
by
Jeremy Leipzig
22k
the samples that are `./.` have no coverage (or not enough to call a genotype) and the `0/0` are homozygous reference
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