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135 results • Page
2 of 3
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1
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2
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297
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Questions Regarding Normalization and Standardization in RNA-seq Differential Analysis
RNA-seq
Normalization
updated 3 days ago by
Ram
44k • written 4 days ago by
wdasda122
▴ 10
1
vote
1
reply
214
views
How to make DiffBind Run Faster?
DiffBind
ATAC-seq
updated 3 days ago by
jared.andrews07
★ 17k • written 3 days ago by
B.N.
▴ 10
1
vote
2
replies
650
views
Question about various of graph format. How to get the sequence and source of a specific node?
vg
3 days ago by
chuanj8848
• 0
1
vote
2
replies
269
views
Illumina RNA-seq: Overrepresented sequences are mostly in the R2 reads, not R1
illumina
rRNA
RNAseq
RNA
updated 3 days ago by
GenoMax
146k • written 3 days ago by
Umberto
▴ 10
1
vote
0
replies
103
views
What is the right choice of normalization and preprocessing before WGCNA using RNAseq data in a cohort?
normalization
RNA_seq
cohort
WGCNA
1 day ago by
sukeshinik5
▴ 50
1
vote
2
replies
1.0k
views
How to find coordinates of TSS from 5pUTR and TTS from 3pUTR in transcriptome/ mRNA ?
coordinates
23 hours ago by
isha.lily20
▴ 10
1
vote
2
replies
227
views
Unexpected High T-Base Content in scRNA-seq Fastq Files and GC Bias Correction
Fastq
Fastqc
scRNA-seq
quality-control
22 hours ago by
Cooper
• 0
1
vote
1
reply
214
views
Comparing whole transcriptome under one condition to the transcriptomes under other conditions
transcriptomics
updated 20 hours ago by
dthorbur
★ 2.5k • written 3 days ago by
Texx
• 0
1
vote
1
reply
103
views
Outlier after DEseq2 in meta-analysis
meta-analysis
rna-seq
outlier
DESeq2
updated 15 hours ago by
Ram
44k • written 23 hours ago by
astefanovic496
▴ 10
1
vote
2
replies
183
views
Reference genome size for genome size estimation.
genome-size
updated 15 hours ago by
Ram
44k • written 1 day ago by
Shakunthala Natarajan
• 0
1
vote
2
replies
170
views
PCA for count data
PCA
updated 14 hours ago by
yura.grabovska
▴ 520 • written 18 hours ago by
QX
▴ 60
1
vote
9
replies
242
views
miRNA mapping with bowtie2 gives low alignment %
bowtie2
alignment
mirna
9 hours ago by
Ant
▴ 20
1
vote
4
replies
289
views
Which Should Take Priority When Selecting DEGs: FDR or Log Fold Change?
DESeq2
logFC
FDR
DEGs
edgeR
updated 3 hours ago by
Gordon Smyth
★ 7.4k • written 1 day ago by
bioinfo1994
▴ 10
0
votes
0
replies
178
views
Forum:
epitope-TCR binding prediction, vaccine design
vaccine
epitope-TCR
binding
4 days ago by
Dara
• 0
0
votes
1
reply
225
views
Aligning to transcriptome with STAR generates error in Salmon sequence length
STAR
Salmon
RNAseq
updated 4 days ago by
Dunois
★ 2.6k • written 4 days ago by
Lena
• 0
0
votes
2
replies
291
views
extracting reads from FASTA/FASTQ file
RNA-seq
RNA
updated 4 days ago by
GenoMax
146k • written 4 days ago by
bleven
• 0
0
votes
2
replies
264
views
all genes have negative logFC edgeR
edgeR
updated 4 days ago by
rfran010
★ 1.3k • written 4 days ago by
xiaoyongli407
• 0
0
votes
0
replies
1.5k
views
METAL meta-analysis software crash
metal
meta-analysis
gwas
updated 5 days ago by
Ty
• 0 • written 4.5 years ago by
ydadmehr
• 0
0
votes
0
replies
168
views
Facing problems in analysis of bisulfite sequencing data
sequencing
Bisulfite
updated 3 days ago by
GenoMax
146k • written 4 days ago by
SHREYA
• 0
0
votes
0
replies
147
views
News:
ONLINE COURSE – Genome Assembly and Annotation (GAAA01)
Annotation
Genome
Assembly
Genomics
updated 6 days ago by
GenoMax
146k • written 6 days ago by
oliverhooker
▴ 110
0
votes
0
replies
167
views
ucsc table browser
ucsc
3 days ago by
daffodil
▴ 10
0
votes
0
replies
170
views
IGV - Load custom variant track
vcf
igv
react
3 days ago by
sadapas
• 0
0
votes
1
reply
217
views
Why are the SINEs annotated as zero when using RepeatModeler + RepeatMasker?
SINEs
Repeatmodeler
RepeatMasker
updated 3 days ago by
Michael
55k • written 3 days ago by
mut
• 0
0
votes
0
replies
161
views
CNVKit batch output
CNVkit
deletion
duplication
3 days ago by
aleksandra.vitkovac97
• 0
0
votes
0
replies
116
views
News:
Eukaryotic Genome Assembly Using PacBio and Hi-C course (4-8 November)
Genome-Assembly
PacBio
Long-reads
Hi-C
5 days ago by
carlopecoraro2
★ 2.6k
0
votes
0
replies
171
views
Advisable to perform GSVA on single cells?
GSVA
scRNA-seq
3 days ago by
bio_info
▴ 20
0
votes
0
replies
169
views
Small rna library analysis
Sirna
small-rna
updated 3 days ago by
Ram
44k • written 3 days ago by
martta95
▴ 10
0
votes
0
replies
175
views
Statistical test to be used for dataset
biostatistics
statistical-test
updated 3 days ago by
Ram
44k • written 3 days ago by
odi
▴ 10
0
votes
2
replies
278
views
Snakemake - pipeline shut down without error
snakemake
3 days ago by
bhumm
▴ 170
0
votes
0
replies
14
views
merging of two assemblies from different short-reads techniques
illumina
assembly
DNBSEQ
hybrid
1 hour ago by
Andrew Yu
• 0
0
votes
0
replies
165
views
News:
Online Workshop - A Practical Introduction to NGS Data Analysis (December 9-11, 2024)
Workshop
Variant-Calling
RNA-Seq
Illumina
DNA-Seq
updated 3 days ago by
Ram
44k • written 3 days ago by
ecSeq Bioinformatics
• 0
0
votes
1
reply
199
views
validation approach for CNVs
CNV
updated 3 days ago by
Pierre Lindenbaum
164k • written 3 days ago by
heureuse
• 0
0
votes
0
replies
168
views
Error While Using BSmooth in bsseq
error
bsmooth
WGBS
bsseq
methylation
3 days ago by
izmitli_biyoinformatikçi
• 0
0
votes
0
replies
167
views
Cytoscape - stringApp terms could not be mapped to any identifier
stringApp
nodes
Cytoscape
terms
bug
3 days ago by
Jordan
• 0
0
votes
1
reply
186
views
News:
Course: Single-cell RNA-seq analysis with R/Bioconductor
Bioconductor
single-cell-RNAseq
updated 6 days ago by
yura.grabovska
▴ 520 • written 6 days ago by
carlopecoraro2
★ 2.6k
0
votes
4
replies
340
views
Grenedalf - error reads sam, bam, sync files
Grenedalf
pool-seq
updated 3 days ago by
Ram
44k • written 19 days ago by
Elizabeth
▴ 30
0
votes
0
replies
168
views
Issues with RAT in CAT_pack and Optimizing Relative Abundance Calculation
metagenomics
taxonomy
mag
annotation
3 days ago by
LuciaNhu
• 0
0
votes
6
replies
981
views
miRNAseq - over-presented sequence in negative control
miRNAseq
adaptor
dimer
updated 5 days ago by
Ant
▴ 20 • written 13 months ago by
MH85
▴ 20
0
votes
0
replies
129
views
Checking Sequence Duplication or errors in a de novo transcriptome assembly
DuplicatedSequences
assemblyError
redundantSequences
deNovoTranscriptome
6 days ago by
Vin Dee
• 0
0
votes
0
replies
6
views
gtf files for various organism in ucsc
gtf
10 minutes ago by
1769mkc
★ 1.2k
0
votes
1
reply
208
views
STRUCTURE runs failing: core dumping and slurm exit code 10?
slurm
linux
STRUCTURE
updated 3 days ago by
GenoMax
146k • written 3 days ago by
katherinedrotos
• 0
0
votes
3
replies
326
views
Different annotations for different isoforms from the same gene
metatranscriptomics
Trinity
RNA-seq
Isoform
updated 3 days ago by
Dunois
★ 2.6k • written 4 days ago by
Chikae
• 0
0
votes
0
replies
133
views
News:
Online Workshop - Bioinformatics Pipeline Development with Nextflow (November 13-15, 2024)
Workshop
Nextflow
RNA-Seq
5 days ago by
ecSeq Bioinformatics
• 0
0
votes
0
replies
118
views
Differential expression analysis from .chp files with Limma
expression
limma
IonTorrent
differential
5 days ago by
Rogerio Ribeiro
▴ 110
0
votes
1
reply
222
views
co-occurrence matrix from my VCF file
co-occurrence
vcf
updated 5 days ago by
robben
• 0 • written 6 days ago by
HarperReed
• 0
0
votes
0
replies
166
views
A question with interpreting heatmaps from limma
RNA-seq
limma
updated 2 days ago by
Ram
44k • written 3 days ago by
lhwh1208
• 0
0
votes
0
replies
174
views
News:
Machine Learning for Multi-Omics Integration (online course) -January 13-15, 2025
Machine-Learning
Big-Data
Multi-Omics
Data-Integration
Deep-Learning
updated 2 days ago by
Ram
44k • written 3 days ago by
carlopecoraro2
★ 2.6k
0
votes
1
reply
190
views
Allele frequency plot : imputed vs reference panel variants
imputation
genotyping
reference
updated 5 days ago by
BlastedBadger
▴ 160 • written 6 days ago by
hello_genome
• 0
0
votes
3
replies
451
views
batch correction limma package (bead based assay data)
batch-correction
updated 1 day ago by
ATpoint
85k • written 6 days ago by
MC_J
• 0
0
votes
1
reply
290
views
What is more important for Structural Variant Calling? Recall or Precision?
structural-variants
merging
precision-recall
updated 1 day ago by
GenoMax
146k • written 6 months ago by
Luke
• 0
135 results • Page
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Recent Votes
A: Filtering Fasta Sequences By Chromosomes Names From A Big Fasta File
Answer: What is wrong with my scripts?
Answer: What is wrong with my scripts?
Answer: What is wrong with my scripts?
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Merged analysis of microarray datasets using R
Outlier after DEseq2 in meta-analysis
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Comment: Split vcf file to fit tbi requirements
by
cassandriatayfernandez
• 0
Hi there, I just checked and it doesn't work with a csi index and they have no intention of adding that functionality unfortunately. I tr…
Comment: Which Should Take Priority When Selecting DEGs: FDR or Log Fold Change?
by
Gordon Smyth
★ 7.4k
Because it is too simplistic to focus on one factor (logFC) in isolation, instead of considering logFC, dispersion and expression level all…
Comment: PyMOL scripting with GPUs on LSF
by
noodle
▴ 590
I think this is outdated, we're up to pymol 3 now!
Comment: PyMOL scripting with GPUs on LSF
by
GenoMax
146k
https://pymol.org/support-platforms.html? does not mention support for GPU's as far as compute goes.
Comment: Issue with Downloading Genomes from BVBRC
by
GenoMax
146k
You will have to email the group that manages the site to see what is going on. Sometimes website refreshes go wrong and perhaps that direc…
Comment: What is wrong with my scripts?
by
nuorain
▴ 30
Thank you for your comments.
Comment: What is wrong with my scripts?
by
nuorain
▴ 30
Thank you so much. It works now.
Comment: Blast Settings For Short Sequences
by
Ethan
• 0
Thanks Kevin. This option also worked well for me :)
Comment: Issue with Downloading Genomes from BVBRC
by
lifengyi
• 0
I'm using the BV-BRC ftp site for the first time, and run into the same issue. So, I checked the ftp site with `curl` command and found th…
Comment: Cluster regions based on similar/dissimilar ChIP-seq signal profile across the w
by
Ming Tommy Tang
★ 4.4k
Take a look at https://github.com/jokergoo/ComplexHeatmap/issues/57 I am writing a long blog post for all things related to ChIPseq heatmap.
Comment: miRNA mapping with bowtie2 gives low alignment %
by
Ant
▴ 20
Okay, I will do that. Thanks a lot for your time and help. I will talk to them and get back with the answer.
Answer: What is wrong with my scripts?
by
Ming Tommy Tang
★ 4.4k
add data.format="bcr xml" in the GDCquery()
Answer: Cluster regions based on similar/dissimilar ChIP-seq signal profile across the w
by
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4.3k
You can pull the `ScaleRegion` data directly into scikit learn: ```python import pandas as pd import numpy as np import sklearn da…
Comment: Merge VCF files by chromosome and Across samples
by
Pierre Lindenbaum
164k
https://nf-co.re/sarek/3.4.4
Comment: Merge VCF files by chromosome and Across samples
by
Pierre Lindenbaum
164k
> the sole reason to split the chromosomes is to save time. you don't save time when creating a new bam when GATK can use intervals.
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