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50 results • Page
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Showing top results for tag:
rna
•
reset
0
votes
0
replies
170
views
Blog:
The Complete Guide to Metatranscriptome Sequencing
RNA
8 days ago by
Novogene
▴ 460
3
votes
2
replies
233
views
Downloading Raw Reads
reads
RNA
updated 9 days ago by
colindaven
6.8k • written 10 days ago by
Jamie
• 0
1
vote
2
replies
372
views
Illumina RNA-seq: Overrepresented sequences are mostly in the R2 reads, not R1
illumina
rRNA
RNAseq
RNA
updated 20 days ago by
GenoMax
146k • written 20 days ago by
Umberto
▴ 10
0
votes
2
replies
346
views
extracting reads from FASTA/FASTQ file
RNA-seq
RNA
updated 21 days ago by
GenoMax
146k • written 21 days ago by
bleven
• 0
0
votes
1
reply
262
views
DeSeq2 filter transcripts
DeSeq2
RNA-seq
RNA
updated 21 days ago by
seidel
11k • written 21 days ago by
bleven
• 0
3
votes
1
reply
424
views
Chemistry Detection Error in CellRanger for Single-Cell RNA-Seq Data
cellranger
single-cell
RNA
updated 8 weeks ago by
GenoMax
146k • written 8 weeks ago by
97sun3
▴ 10
0
votes
4
replies
359
views
Heatmap for DEGs
seq
heatmap
RNA
9 weeks ago by
4732b159
• 0
1
vote
1
reply
330
views
WGCNA - dendogram: How to interpret alterations of clusters
clustering
transcriptomics
WGCNA
rna
updated 9 weeks ago by
Ram
44k • written 10 weeks ago by
christiantd
• 0
0
votes
1
reply
394
views
Book about RNA structure
RNA
updated 10 weeks ago by
Mensur Dlakic
★ 28k • written 11 weeks ago by
bef1
• 0
1
vote
1
reply
292
views
Testing for specific genes of whole RNA Sequencing
R
DESeq2
Sequencing
RNA
updated 11 weeks ago by
ATpoint
85k • written 11 weeks ago by
hagl
▴ 20
3
votes
2
replies
303
views
Extraction of miRNA Sequences from Infernal cmscan Output Using Python
infernal
assembly
rna
genome
mirna
updated 11 weeks ago by
massa.kassa.sc3na
▴ 630 • written 11 weeks ago by
Vijith
▴ 60
0
votes
1
reply
220
views
Multiple annotation in my table counts
RNA-seq
RNA
microRNA
miRNAs
12 weeks ago by
omicon
• 0
4
votes
5
replies
566
views
DESeq2 results vs. shrinkage results
Shrinkage
DESeq2
Sequencing
RNA
updated 3 months ago by
i.sudbery
20k • written 3 months ago by
hagl
▴ 20
1
vote
3
replies
397
views
retrieve genomic positions and chromosome number for a list of genes
position
seq
genomic
RNA
updated 3 months ago by
Pierre Lindenbaum
164k • written 3 months ago by
Fatemeh
▴ 40
0
votes
1
reply
337
views
High Amount of UnAssignedNoFeatures in FeatureCounts Output
rna
star
featurecount
updated 3 months ago by
Ram
44k • written 3 months ago by
Tom Brady
• 0
1
vote
7
replies
662
views
How do decide if a processed scRNA-seq data is read counts or UMI format ?
scanpy
python
single-cell
anndata
RNA
updated 3 months ago by
ATpoint
85k • written 3 months ago by
JACKY
▴ 160
2
votes
17
replies
1.4k
views
RNA STAR and trimming
trimming
STAR
RNA-seq
RNA
updated 3 months ago by
GenoMax
146k • written 3 months ago by
casio
▴ 10
0
votes
3
replies
303
views
Filterbytile.sh - Exception in thread "main" java.lang.RuntimeException: Can't read file ...
Illumina
filterbytile
Java
RNA
updated 3 months ago by
GenoMax
146k • written 3 months ago by
duplessisantzel
• 0
0
votes
3
replies
626
views
RNA virus (HIV, HCV, Influenza, or SARS-CoV-2) datasets with corresponding fitness values.
RNA
updated 4 months ago by
Ram
44k • written 4 months ago by
jimmysibandah
• 0
0
votes
1
reply
438
views
What tools are there to quantify m6A methylation of Nanopore bam files?
m6a
methylation
Nanopore
RNA
updated 4 months ago by
Ram
44k • written 4 months ago by
smb51095
• 0
2
votes
6
replies
670
views
Finding scRNA-seq datasets of healthy human ovaries
python
GEO
single-cell
RNA
updated 4 months ago by
Ram
44k • written 4 months ago by
JACKY
▴ 160
5
votes
4
replies
680
views
Tool:
Neurosnap: Platform for making access to bioinformatic tools as simple as possible
protein
docking
rna
transcriptome
toxicity
updated 4 months ago by
Kevin
▴ 90 • written 4 months ago by
keaun
▴ 40
1
vote
2
replies
437
views
finding housekeeping genes and small RNA sequences of Arabidopsis thaliana
housekeeping-genes
RNA
4 months ago by
analyst
▴ 50
0
votes
3
replies
625
views
Transcriptome analysis of virus infected plants and their controls
DEG
heatmap
rna
updated 4 months ago by
manaswwm
▴ 540 • written 4 months ago by
diya
• 0
3
votes
2
replies
372
views
Combining microarray, RNA Seq, whole & exome sequencing
Microarray
RNA
updated 5 months ago by
i.sudbery
20k • written 5 months ago by
Bine
▴ 70
0
votes
3
replies
447
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 5 months ago by
noodle
▴ 590 • written 5 months ago by
doramora
▴ 10
0
votes
2
replies
394
views
Error in plotting PCA plot in seurat
PCA
single-cell
seurat
scRNA
RNA
updated 5 months ago by
Ram
44k • written 5 months ago by
Sumeet
• 0
5
votes
12
replies
1.1k
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 5 months ago by
i.sudbery
20k • written 5 months ago by
Assa Yeroslaviz
★ 1.9k
3
votes
3
replies
542
views
What analysis suitable to identify similarly expressed genes between two samples (treated vs untreated). Contrary to DGE analysis,
Gene-Expression
RNA
NOISeq
DGE
updated 6 months ago by
ATpoint
85k • written 6 months ago by
alifafiq1
• 0
0
votes
0
replies
263
views
Designing single-stable RNA molecules
structure
RNA
6 months ago by
Edna
• 0
0
votes
0
replies
194
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 6 months ago by
Ram
44k • written 6 months ago by
Amélie
• 0
0
votes
0
replies
213
views
meta-analysis on RNA seq AND microarray results
microarray
RNA
7 months ago by
liuyibin2005
• 0
0
votes
0
replies
253
views
MIENTURNET - miRNA enrichment analysis
miRNA-enrichment
mRNA
RNA
updated 7 months ago by
Ram
44k • written 7 months ago by
PBC
▴ 10
31
votes
14
replies
12k
views
11 follow
Finding Rrna Genes In Metagenomic Data
rna
rRNA
metagenomics
updated 7 months ago by
Ram
44k • written 14.0 years ago by
toshnam
▴ 650
0
votes
0
replies
191
views
A way to read both the DNA fragment and the nascent RNA
ChRO-seq
RNA
transcription
NET-seq
nascent
8 months ago by
Chris
• 0
1
vote
4
replies
617
views
How can I get the sequences of the first 20nt of introns and the last 250nt of introns of hg38 genome?
annotation
RNA
updated 8 months ago by
Juke34
8.8k • written 8 months ago by
xiaoleiusc
▴ 140
0
votes
3
replies
616
views
Normalization of combined normal and tumor tissue samples from GTEx and TCGA prior to CIBERSORTx devconvolution
gtex
cibersort
tcga
rna
normalization
updated 8 months ago by
jv
★ 1.8k • written 8 months ago by
star
▴ 10
14
votes
3
replies
1.7k
views
is oxford nanopore technology data paired or single end sequencing?
oxford-nanopore
DNA
RNA
updated 8 months ago by
Ram
44k • written 9 months ago by
Alewa
▴ 170
0
votes
0
replies
647
views
Is there a RSeQC manual or guide
RSeQC
RNA
9 months ago by
gallardodiazmiriam
▴ 20
0
votes
1
reply
471
views
RNA Type Detection
rna-seq
rna
types
9 months ago by
kyildizn
• 0
3
votes
4
replies
858
views
Differential RNA editing using edgeR
editing
RNA
GLM
9 months ago by
Aiswarya
▴ 20
4
votes
2
replies
487
views
Using Expression of a Gene as a Linear Regression Variable
rna
updated 9 months ago by
i.sudbery
20k • written 9 months ago by
jamie3355
• 0
0
votes
0
replies
336
views
Generating a Scores Plot From RNA-Seq Data
Sequencing
Plotting
RNA-Seq
RNA
10 months ago by
robert.flynn.21
▴ 10
0
votes
2
replies
565
views
Why does the Pair-End RNA library exhibit a significant disparity between the mapping results of R2 compared to R1?
illumina
pair-end
r2
rna
updated 10 months ago by
GenoMax
146k • written 10 months ago by
Carolina
• 0
1
vote
5
replies
784
views
Normalization of RNA captureSeq data (<20 genes captured)
captureSeq
edgeR
DESeq2
RNA
ERCC
updated 10 months ago by
ATpoint
85k • written 10 months ago by
jips
• 0
0
votes
0
replies
343
views
scVelo cell transitions from marker gene expressing cells
velocity
scvelo
RNA
11 months ago by
rbronste
▴ 420
8
votes
10
replies
1.5k
views
Can I estimate RNA velocity in Visium Spatial Gene Expression for FFPE
Visium
RNA
9 months ago by
oghzzang
▴ 50
6
votes
6
replies
1.2k
views
6 follow
STAR alignment speed
STAR
alignment
RNA
updated 11 months ago by
ATpoint
85k • written 11 months ago by
Gilles
▴ 10
0
votes
0
replies
367
views
Which of the following relationships is correct for making a hypothetical ceRNA?
cancer
lncRNA
ceRNA
RNA
miRNA
11 months ago by
mohammadhassanj
▴ 260
1
vote
3
replies
603
views
DNA/RNA Sequence Alignment
dna
rna
alignment
sequence
updated 11 months ago by
Mensur Dlakic
★ 28k • written 11 months ago by
Mirza
• 0
50 results • Page
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Recent Votes
Comment: Can a read be aligned more than once?
Answer: How to find the adapter sequence of an RNAseq dataset?
A: RNA-seq data analysis
Answer: How to solve DESeq2 Error in checkFullRank(modelMatrix)?
Answer: How to find the adapter sequence of an RNAseq dataset?
Answer: featureCounts strand specificity
Answer: featureCounts strand specificity
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Recent Replies
Comment: Repeat CT in overrepresented sequences
by
GenoMax
146k
> fastqc keeps identifying overrepresented sequences consisting of C and T. Which read is it located in? `fastqc` is of limited utility wi…
Comment: How to solve DESeq2 Error in checkFullRank(modelMatrix)?
by
DOBI
• 0
Thank you so much for your response, and apologies for the delayed reply! Your explanation really clarified things—I’ll check out the secti…
Answer: How to find the adapter sequence of an RNAseq dataset?
by
GenoMax
146k
Looks like you are doing this analysis via Galaxy so the following may not help immediately. You can always post to Galaxy help forum for s…
Answer: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How?
by
teofoskol
• 0
There are few ways, but you can't be 100% sure. 1st you can try to normilize with SCTransform (suppossed to remove some of the batch effect…
Answer: filterx : fast and efficient filter tool written in Rust for csv,fasta,fastq,gff
by
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v0.0.2 has full platform supported now :) ! [https://github.com/dwpeng/filterx/releases/tag/v0.0.2][1] ![enter image description he…
Comment: HTSeq-count vs. FeatureCounts: Significant Difference in Results
by
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▴ 10
omg, you are amazing! Yes, that's the problem! The bam file was in default coordinate sort since I use samtools sort default parameters. …
Comment: R encountering fatal error and quitting the session
by
dthorbur
★ 2.5k
Can you watch memory utilisation as you run the model? Task manager on windows works.
Comment: Magnesium ion in a post-docking adjustment
by
dthorbur
★ 2.5k
[`AlphaFold3`](https://alphafoldserver.com/) (assuming you're not at conflict with their terms of use) can handle both ligands and ions. An…
Answer: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How?
by
ATpoint
85k
> But How could I know if the difference comes from sample instead of sequencing runs or cohort-driven batch effect? You cannot. It's pe…
Comment: Comparing GSEA mutant data to wild type
by
conmul
• 0
Sorry that it was unclear in the post. The data is all CRISPR gene effect scores from DepMap. The 'significant genes' as mentioned in the p…
Comment: How to determine whether it is 10x data
by
king
• 0
Thank you for your answer, it's very inspiring.
Comment: Inquiry about depth of coverage and copy number variation
by
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• 0
Thanks Pierre, I was actually thinking about the duplicate PCR reads and didn't explain it properly. I have found a post mentioning that qu…
Comment: Can a read be aligned more than once?
by
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146k
Yes a read can be aligned more than once (I don't specifically know about gam/gaf). It would be called a "multi-mapping" read. You could im…
Comment: Statistical test to be used for dataset
by
allingt
• 0
The choice of test depends on the types of variables involved and the hypothesis you have. But most importantly on the question you want am…
Comment: dittoHeatmap; adding column labels on the heatmap
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★ 18k
I'd consider making a [block annotation](https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#block-annotation…
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