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1,068 results • Page
2 of 22
Sort: Rank
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Votes
Replies
0
votes
4
replies
251
views
Introduce SNPs on FASTA
simulation
snps
haplotypes
pharmacogenetics
updated 2 days ago by
Michael
54k • written 2 days ago by
Riccardo
▴ 10
0
votes
0
replies
120
views
barcode of TCR-sequencing
barcode
2 days ago by
yueli7
▴ 250
0
votes
0
replies
119
views
News:
Online course: Meta-analysis in R - last 2 seats left
Meta-Analysis
Statistics
R
updated 2 days ago by
Ram
43k • written 2 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
116
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 2 days ago by
Ram
43k • written 2 days ago by
Alexandros
• 0
0
votes
1
reply
156
views
unable to get feature count results
featureCounts
updated 2 days ago by
Ram
43k • written 2 days ago by
Ravita
• 0
0
votes
3
replies
260
views
KEGG Pathways
r
RNA-seq
updated 2 days ago by
Ram
43k • written 2 days ago by
Sudip
• 0
4
votes
6
replies
3.8k
views
Taking the difference of two VCFs (or removing singletons)
genome
sequencing
singleton
SNP
filter
updated 2 days ago by
Andres
▴ 20 • written 9.6 years ago by
hermathena
▴ 40
0
votes
0
replies
123
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
2 days ago by
Bine
▴ 60
0
votes
1
reply
272
views
News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
2 days ago by
David Langenberger
11k
0
votes
0
replies
123
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
2 days ago by
8armed
• 0
0
votes
1
reply
175
views
Deseq2
Deseq2
updated 2 days ago by
Jack Tierney
▴ 360 • written 2 days ago by
Sudip
• 0
1
vote
1
reply
204
views
Polishing genome assembly
polishing
Nanopore
PacBio
updated 2 days ago by
Michael
54k • written 2 days ago by
Lissa Cruz Saavedra
• 0
5
votes
3
replies
249
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 2 days ago by
Lluís R.
★ 1.2k • written 2 days ago by
이민경[학생](대학원 융합의과학과)
• 0
2
votes
2
replies
180
views
MA plot of shrunken fold change
MA-plot
Deseq2
updated 2 days ago by
ATpoint
82k • written 2 days ago by
Sudip
• 0
1
vote
2
replies
211
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 2 days ago by
Ram
43k • written 2 days ago by
Ravita
• 0
0
votes
0
replies
105
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
2 days ago by
Adyasha
• 0
0
votes
0
replies
108
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
2 days ago by
fanglujing
▴ 60
0
votes
0
replies
123
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
2 days ago by
Jacob
• 0
0
votes
3
replies
726
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 2 days ago by
weidonglu
• 0 • written 21 months ago by
JZX
• 0
0
votes
4
replies
245
views
Perfom a Gene Ontology Analysis from GO terms txt file
RNA-Seq
GO
updated 2 days ago by
Ram
43k • written 2 days ago by
Hamtaro
▴ 50
0
votes
1
reply
173
views
Differential Accessibility
DiffBind
updated 2 days ago by
Ram
43k • written 2 days ago by
Shloka
• 0
0
votes
3
replies
264
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 2 days ago by
GenoMax
142k • written 2 days ago by
kim
• 0
3
votes
2
replies
356
views
Extract protein sequence
fasta
alignment
blast
1 day ago by
anna
▴ 20
3
votes
3
replies
305
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 3 days ago by
noodle
▴ 580 • written 3 days ago by
WUSCHEL
▴ 750
0
votes
1
reply
158
views
metagenomic virome quality assessment
viromics
metagenomics
updated 3 days ago by
Ram
43k • written 3 days ago by
Petchimuthu
• 0
3
votes
7
replies
305
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
3 days ago by
salias
• 0
0
votes
0
replies
120
views
Using limma in methylation EM-seq?
EM-seq
methylation
3 days ago by
Lluís R.
★ 1.2k
4
votes
7
replies
565
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
3 days ago by
e.r.zakiev
▴ 210
0
votes
0
replies
119
views
Synteny analysis
bacterial
synteny
genome
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Namil
• 0
0
votes
4
replies
230
views
Genbank File Format
gbkformat
2 days ago by
alenew.am
• 0
0
votes
5
replies
394
views
How should I make kallisto indexes?
kallisto
updated 3 days ago by
dsull
★ 5.9k • written 17 days ago by
bioinfo
▴ 150
0
votes
0
replies
213
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
3 days ago by
SSSJec
• 0
0
votes
3
replies
202
views
Software to separate reads from different individuals
software
development
nanopore
updated 2 days ago by
GenoMax
142k • written 3 days ago by
njornet
▴ 20
0
votes
0
replies
90
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
3 days ago by
David
• 0
4
votes
5
replies
278
views
High Malat-1 expression in single cell data
cell
analysis
single
updated 3 days ago by
dsull
★ 5.9k • written 3 days ago by
Kazo
▴ 10
0
votes
2
replies
187
views
How to update R on ubuntu
installation
update
R
apt-get
3 days ago by
Bosberg
▴ 50
4
votes
0
replies
127
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
3 days ago by
Biostar
2.7k
0
votes
1
reply
128
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Ruqaiya
• 0
0
votes
1
reply
270
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 3 days ago by
trausch
★ 1.9k • written 19 days ago by
zec018
• 0
0
votes
0
replies
99
views
LEfSe
LEfSe
3 days ago by
benkosta
• 0
0
votes
0
replies
85
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
3 days ago by
Sara
▴ 30
1
vote
4
replies
375
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
3 days ago by
hagl
▴ 10
0
votes
4
replies
225
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
3 hours ago by
matteo.levorato
• 0
0
votes
2
replies
147
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
3 days ago by
Lluís R.
★ 1.2k
0
votes
1
reply
137
views
How to solve DESeq2 Error in checkFullRank(modelMatrix)?
RNA-Seq
DESeq2
updated 3 days ago by
i.sudbery
19k • written 3 days ago by
DOBI
• 0
0
votes
0
replies
96
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
3 days ago by
atharvakarkare14
▴ 30
5
votes
16
replies
673
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
3 days ago by
Ruqaiya
• 0
0
votes
2
replies
192
views
What should I consider as FASTA for dataset?
PDB
FASTA
2 days ago by
Nafi
• 0
38
votes
24
replies
1.8k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 2 days ago by
i.sudbery
19k • written 4 days ago by
noodle
▴ 580
0
votes
0
replies
86
views
Differential accessibility using DiffBinf
diffbind
3 days ago by
Shloka
• 0
1,068 results • Page
2 of 22
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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yvonnehhe
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curious
▴ 750
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jared.andrews07
★ 16k
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Recent Replies
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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