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1,000 results • Page
5 of 20
Sort: Rank
Rank
Views
Votes
Replies
8
votes
16
replies
931
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 6 days ago by
bk11
★ 2.4k • written 8 weeks ago by
Sofia
• 0
0
votes
0
replies
104
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
9 days ago by
ohtang7
▴ 40
3
votes
0
replies
130
views
News:
Interested in Spatial Omics?
Bioconductor
Spatial-Omics
Spatial-Transcriptomics
updated 9 days ago by
Ram
43k • written 9 days ago by
carlopecoraro2
★ 2.5k
2
votes
2
replies
443
views
Using vg gamsort with naive sorting algorithm
gamsort
vg
updated 9 days ago by
Pierre Lindenbaum
161k • written 8 months ago by
AshleeThomson
▴ 80
0
votes
1
reply
174
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 9 days ago by
GenoMax
142k • written 9 days ago by
Srinka
▴ 20
8
votes
5
replies
5.6k
views
ISCN annotation for SV/CN VCF files
SV
written 8 months ago by
a.beggs
▴ 60
0
votes
5
replies
339
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
8 days ago by
njornet
▴ 20
5
votes
4
replies
674
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
8 days ago by
kirillkirilenko
▴ 40
0
votes
0
replies
99
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 9 days ago by
Ram
43k • written 9 days ago by
SHREYA
• 0
0
votes
3
replies
405
views
How to identify gaps in a genome?
awk
seqkit
assembly
fasta
genome
updated 9 days ago by
colindaven
6.4k • written 17 days ago by
rj.rezwan
• 0
0
votes
0
replies
108
views
Merging replicates from Encode project
CHIP-seq
encode
9 days ago by
Nurken
• 0
1
vote
3
replies
250
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
9 days ago by
WouterDeCoster
47k
0
votes
3
replies
236
views
Help for coding: Trinity for differential gene expression studies
Gene
updated 9 days ago by
mchour
• 0 • written 9 days ago by
rhossen
• 0
1
vote
1
reply
174
views
WGCNA preservation analysis
WGCNA
preservation
updated 9 days ago by
Michael
54k • written 9 days ago by
michael.flower.14
▴ 180
1
vote
3
replies
284
views
some error in building kraken2 database
metagenome
kraken2
8 days ago by
Art1ess
• 0
0
votes
1
reply
164
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 9 days ago by
bk11
★ 2.4k • written 9 days ago by
Susmita Mandal
▴ 110
0
votes
1
reply
149
views
Plots for DNA methylation data
plots
DNA
methylation
updated 9 days ago by
GenoMax
142k • written 9 days ago by
sarahawan92
▴ 10
0
votes
3
replies
520
views
python file for coding potential calculator
cpc2.py
updated 9 days ago by
atharvakarkare14
▴ 30 • written 13 days ago by
Ashok
• 0
1
vote
1
reply
184
views
Failed kmer content
kmer
illumina
ngs
updated 9 days ago by
Ram
43k • written 9 days ago by
Kasturi
• 0
0
votes
0
replies
171
views
Forum:
Improvement on automatic annotation of single-cell RNA-seq data from the literature using LLM
annotation
scRNA
llm
9 days ago by
yxwucq
• 0
0
votes
0
replies
96
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 9 days ago by
Ram
43k • written 9 days ago by
SSSJec
• 0
0
votes
6
replies
354
views
How to slice a gvcf file with tabix?
Tabix
bed
gvcf
8 days ago by
Sd
• 0
0
votes
2
replies
195
views
Help with Base quality Score Recalibration (BQSR) using GATK
GATK
BQSR
9 days ago by
sainavyav22
• 0
0
votes
1
reply
153
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 9 days ago by
Ram
43k • written 9 days ago by
Cameron.walker9900
• 0
0
votes
8
replies
364
views
Error in cnetplot enrichplot package
R
updated 9 days ago by
Ram
43k • written 9 days ago by
Farhad
• 0
3
votes
9
replies
494
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 8 days ago by
Istvan Albert
100k • written 9 days ago by
Κοσμάς
• 0
0
votes
0
replies
113
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 9 days ago by
Ram
43k • written 9 days ago by
maxime.policarpo
▴ 200
3
votes
3
replies
216
views
Genbank vs SRA
ncbi
genbank
genomics
sra
updated 9 days ago by
Mensur Dlakic
★ 27k • written 9 days ago by
c_u
▴ 520
0
votes
0
replies
98
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 9 days ago by
Ram
43k • written 9 days ago by
sansan_96
▴ 80
0
votes
0
replies
104
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 9 days ago by
Ram
43k • written 9 days ago by
Amélie
• 0
0
votes
0
replies
206
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 9 days ago by
Ram
43k • written 10 days ago by
Oak
▴ 10
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 9 days ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
2
votes
4
replies
271
views
from row count to tpm
tpm
row-count
normalization
updated 2 days ago by
Ram
43k • written 10 days ago by
michelafrancesconi9
▴ 20
1
vote
8
replies
438
views
Downsampling fastq file
downsample
fastq
2 days ago by
marco.barr
▴ 90
2
votes
3
replies
349
views
How to establish haplotype-specific gene expression levels
RNA-seq
Haplotype
updated 6 days ago by
dsull
★ 5.9k • written 23 days ago by
javanokendo
▴ 60
0
votes
1
reply
144
views
tbtool
tbtool
updated 10 days ago by
Ram
43k • written 10 days ago by
Raman
• 0
0
votes
10
replies
479
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 2 days ago by
i.sudbery
19k • written 10 days ago by
Patadu94
• 0
3
votes
3
replies
244
views
Getting the nucleotide sequence of proteins, having their UniProt IDs
Nucleotide
Genomic
Sequence
Uniprot
Proteins
updated 10 days ago by
GenoMax
142k • written 10 days ago by
Mariana
▴ 40
0
votes
1
reply
137
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 10 days ago by
ATpoint
82k • written 10 days ago by
enanoide
• 0
0
votes
0
replies
92
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
10 days ago by
manaswwm
▴ 510
3
votes
3
replies
731
views
KissDE and batch effect
kissDE
kissplice
10 days ago by
david.b.rombaut
▴ 10
0
votes
0
replies
82
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
9 days ago by
alifafiq1
• 0
76
votes
72
replies
19k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
7 days ago by
Kevin Blighe
87k
0
votes
0
replies
88
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
10 days ago by
feather-W
• 0
2
votes
4
replies
316
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
8 days ago by
samuelkalandarov2002
▴ 10
0
votes
0
replies
89
views
Annotating single cell data automatically
cell
annotation
single
10 days ago by
Gerard
• 0
0
votes
0
replies
92
views
News:
Online course: DNA methylation
Pacbio
Nanopore
DnaMethylation
Evolution
10 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
145
views
Job:
Ensembl Plants Senior Bioinformatician
ebi
embl
genomics
ensembl
10 days ago by
Ben_Ensembl
★ 2.4k
2
votes
4
replies
342
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
8 days ago by
HyperEvo
• 0
0
votes
1
reply
171
views
RNA-seq bacteria contamination
RNA-seq
updated 10 days ago by
GenoMax
142k • written 10 days ago by
sh
• 0
1,000 results • Page
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Recent Votes
Comment: How to access TCGA samples that were treated with a specific drug?
C: GATK genomicsDBimport intervals for WGS
Comment: DiffBind: no peaks in DBA
Comment: When should I NOT apply batch correction for my single-cell RNAseq data?
Comment: Bacterial plasmid analysis
Answer: Problem with data downloaded from Short Reads Archive (SRA)
Answer: Super ehancers
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Comment: DiffBind: no peaks in DBA
by
yvonneh
▴ 10
Ok fixed!
Comment: Extract gRNA sequence using cutadapt
by
GenoMax
142k
Can you try lowering the `k` to `k=9`? You don't have any duplicate sequences in your library file? That may be one reason why bbduk is r…
Comment: Extract gRNA sequence using cutadapt
by
gernophil
▴ 80
This topic is almost 5 years old, but I am facing the same (or at least a very similar) issue. I have ngs files from a CRISPR screen that …
Answer: RNA-seq data for deep learning classification
by
dsull
★ 5.9k
Honestly speaking, if it's deep learning, it probably doesn't matter that much if you use something like TPMs (probably not raw counts, unl…
Comment: How does gene length effect the number of reads mapped
by
Chen
• 0
Thanks for the detailed answer and I really appreciate it! I still have one question about why the number of reads can be influenced by the…
Comment: Split Fastq Files Into Chunks Of 1M Reads
by
thomas.heigl.ibk
• 0
i tried it. it splits, however, when i compare the first 8 lines of the second split file with the according lines from the original file, …
Comment: DiffBind: no peaks in DBA
by
Ram
43k
> I've also included the txt version of my .csv file No, you added a screenshot of plain text content, which is counterproductive. You can…
Comment: How to access TCGA samples that were treated with a specific drug?
by
GenoMax
142k
At the GDC portal you have to turn the "therapeutic agents" toggle under "Clinical Data Analysis" on. ![drug][1] For Breast cancer you c…
Answer: Loss of 'var' using concatenation of AnnData objects
by
Hugo
• 0
Similar question has been asked and answered on [scverse discourse](https://discourse.scverse.org/t/loosing-anndata-var-layer-when-using-sc…
Comment: Bacterial plasmid analysis
by
Zamin Iqbal
▴ 20
Hi Nicole. 1. The clustering will be quite different between pling and the rep types (because plasmids with one rep type can still be ve…
Comment: Do I need to go back and filter my long-reads?
by
Ram
43k
Do not delete posts that have received feedback. Engage with the user providing you feedback.
Answer: Download eQTL data of one specific gene for all tissues from GTEx
by
bk11
★ 2.4k
Please kindly check your result here. You can click `csv` and download the date in this [link][1]. **OR** If you prefer to use R, there i…
Comment: RNAseq one control two conditions, shared and exclusive genes
by
matteo.levorato
• 0
but why not a single matrix with the 3 different condition and then by lfcShrink function get the DEGs of each condition?
Answer: Super ehancers
by
jared.andrews07
★ 16k
Sure, you can run it on them. Stitching tends to happen less frequently since the ATAC peaks are generally less wide than H3K27ac, but it'l…
Answer: What purposes can TPM values be used for?
by
jared.andrews07
★ 16k
TPMs cannot be used for intersample comparisons, but they can be used for intrasample comparisons (e.g. comparing relative expression level…
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