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448 results • Page
4 of 9
Sort: replies
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Views
Votes
Replies
0
votes
2
replies
293
views
Abundance Calculation in MetaPhlAn 3: Methodology, TPM or RPKM, and the Treatment of Unclassified Reads
MetaPhlAn
Normalization
RPKM
TPM
24 days ago by
ramin.k2013
• 0
3
votes
2
replies
1.2k
views
DESeq2 design and Batch effects
RNA-Seq
batch-effect
DESeq2
updated 19 days ago by
Ram
43k • written 4.4 years ago by
baldissera152
▴ 10
0
votes
2
replies
411
views
How can I solve this error?
metal
19 days ago by
22211020193
• 0
1
vote
2
replies
308
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 19 days ago by
Ram
43k • written 19 days ago by
aniigodwinn
• 0
0
votes
2
replies
298
views
RNAseq 1 control 2 different treatment
RNA-seq
21 days ago by
matteo.levorato
• 0
0
votes
2
replies
238
views
BLASTP short sequences (<20aa) - interpreting results
blast
sequence
blastp
alignment
27 days ago by
neish
• 0
2
votes
2
replies
1.8k
views
Parametric or non-parametric tests for qPCR significance testing between treatments?
qPCR
statistical test
parametric
non-parametric
updated 3 days ago by
e.r.zakiev
▴ 210 • written 3.8 years ago by
n.anuragsharma
▴ 40
0
votes
2
replies
238
views
How to detect and visualize ORFs in bacterial genome?
statistics
visualization
ORFs
genome
25 days ago by
marongiu.luigi
▴ 710
1
vote
2
replies
1.9k
views
Remove batch effect from exome data
NGS
exome-sequencing
batch-effect
updated 18 days ago by
Ram
43k • written 6.6 years ago by
Alternative
▴ 270
0
votes
2
replies
452
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
18 days ago by
Ashok
• 0
2
votes
2
replies
295
views
DepMap: siRNA and CRSIPR discrepancy
DepMap
updated 25 days ago by
ATpoint
82k • written 25 days ago by
Shicheng Guo
★ 9.4k
2
votes
2
replies
208
views
PDB related issue
rcsb
pdb
updated 8 days ago by
noodle
▴ 580 • written 8 days ago by
Nafi
• 0
0
votes
2
replies
141
views
Applying the metacell2 algorithm using python
single-cell
scanpy
cells
meta
python
2 hours ago by
JACKY
▴ 140
1
vote
2
replies
219
views
In need of help with my RNA velocity trajectory inference pipeline!
RNAvelocity
28 days ago by
phhelou5
• 0
0
votes
2
replies
277
views
Bedmethyl file format
bedmethyl
methylation
updated 20 days ago by
GenoMax
142k • written 20 days ago by
njornet
▴ 20
1
vote
2
replies
229
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 6 days ago by
Ram
43k • written 7 days ago by
Ravita
• 0
2
votes
2
replies
212
views
Raw counts using stringtie
stringtie
RNA-seq
updated 3 days ago by
GenoMax
142k • written 4 days ago by
ahmad.sajad4541
• 0
0
votes
2
replies
575
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
18 days ago by
航太郎
• 0
0
votes
2
replies
284
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
20 days ago by
mropri
▴ 150
0
votes
2
replies
307
views
bam merging for archaic samples
samtools
bam
updated 16 days ago by
Ram
43k • written 17 days ago by
Matteo Ungaro
▴ 100
1
vote
2
replies
293
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
6 days ago by
Nafi
• 0
1
vote
2
replies
818
views
What type of normalization does removeBatchEffect function require as the input?
batch
limma
removeBatchEffect
rna-seq
batch-effect
updated 20 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
1
vote
2
replies
243
views
convert a seurat object to expressionset
Seurat
26 days ago by
Bine
▴ 60
0
votes
1
reply
188
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 3 days ago by
Ram
43k • written 3 days ago by
Valentina
• 0
1
vote
1
reply
258
views
RNA seq normalization and gene gene correlation
rna-seq
pearson-correlation
vst
updated 25 days ago by
Ram
43k • written 25 days ago by
Fish
• 0
0
votes
1
reply
171
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 18 hours ago by
bk11
★ 2.4k • written 2 days ago by
Yoosef
▴ 60
0
votes
1
reply
273
views
How to do further funtional analysis of DEG KeggGet output list?
KEGGREST
DESEQ2
RNA-Seq
DEG
29 days ago by
joana.maclean
• 0
0
votes
1
reply
240
views
How do I know whether it is not a failure of ChIPseq data
ChIPseq
updated 29 days ago by
dthorbur
★ 1.9k • written 4 weeks ago by
Herman Einstein
• 0
0
votes
1
reply
150
views
Provean help
variant
Provean
updated 4 days ago by
Mensur Dlakic
★ 27k • written 4 days ago by
Arun Sai Kumar
• 0
0
votes
1
reply
203
views
Help with DGEList function
DGEList
R
updated 1 day ago by
marco.barr
▴ 90 • written 3 days ago by
Natali
• 0
1
vote
1
reply
480
views
PLINK multivariable GLM output: p-value without BETA and SE
linear-model
glm
plink
updated 28 days ago by
chrchang523
10k • written 29 days ago by
dsbusiness135
▴ 10
0
votes
1
reply
555
views
Differential Expression Analysis for miRNA
limma
Differential-gene-Expression
miRNA
updated 27 days ago by
Ram
43k • written 3.0 years ago by
Al
• 0
0
votes
1
reply
178
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 13 days ago by
Mensur Dlakic
★ 27k • written 13 days ago by
benguyarenbeyaz98
• 0
0
votes
1
reply
153
views
tbtool
tbtool
updated 14 days ago by
Ram
43k • written 14 days ago by
Raman
• 0
3
votes
1
reply
281
views
how to change the gene header names in a fasta file?
fasta
bioawk
awk
seqkit
updated 25 days ago by
Ram
43k • written 25 days ago by
rj.rezwan
• 0
2
votes
1
reply
264
views
VEP annotation --per_gene allele choice
VEP
updated 24 days ago by
Ram
43k • written 25 days ago by
atariw
▴ 10
1
vote
1
reply
184
views
Failed to download data from EBI with ascp
EBI
aspera
updated 26 days ago by
GenoMax
142k • written 26 days ago by
biock
▴ 60
0
votes
1
reply
294
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 19 days ago by
GenoMax
142k • written 19 days ago by
ycts
• 0
0
votes
1
reply
285
views
cibersort. problem
cibersort
gema122
updated 28 days ago by
Ram
43k • written 4 weeks ago by
gem1
• 0
0
votes
1
reply
182
views
RNA-seq bacteria contamination
RNA-seq
updated 15 days ago by
GenoMax
142k • written 15 days ago by
sh
• 0
0
votes
1
reply
1.1k
views
Ensembl assembly choice for RNA-Seq reference mapping
RNA-Seq
ensembl
STAR
alignment
Assembly
updated 25 days ago by
AHerik
▴ 20 • written 5.0 years ago by
eoin
▴ 30
0
votes
1
reply
228
views
Subsetting and merging back Seurat Object brings different results
Seurat
5 days ago by
Bine
▴ 60
0
votes
1
reply
146
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 15 days ago by
ATpoint
82k • written 15 days ago by
enanoide
• 0
0
votes
1
reply
174
views
How do I run fastq-dump on multiple prefetched files at once?
sratoolkit
fastq-dump
updated 29 days ago by
Pierre Lindenbaum
161k • written 29 days ago by
biotrekker
▴ 100
0
votes
1
reply
121
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 3 hours ago by
andres.firrincieli
3.6k • written 1 day ago by
Antonio
• 0
0
votes
1
reply
210
views
Freyja plot error
Freyja
updated 19 days ago by
Ram
43k • written 20 days ago by
Adyasha
• 0
0
votes
1
reply
184
views
Differential Accessibility
DiffBind
updated 7 days ago by
Ram
43k • written 7 days ago by
Shloka
• 0
0
votes
1
reply
216
views
Finding batch and outlayers
Pca
updated 8 days ago by
christopher medway
▴ 460 • written 8 days ago by
Tigran
• 0
1
vote
1
reply
248
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 11 days ago by
ATpoint
82k • written 11 days ago by
AaronJaime
• 0
0
votes
1
reply
1.3k
views
About BatchQC packages error
Batch-effect
R
updated 19 days ago by
Ram
43k • written 6.1 years ago by
Jun
• 0
448 results • Page
4 of 9
Recent Votes
Comment: Repeated testing/data mining in RNA Seq
Comment: UMI-Tools knee-method has great influence on the results of white list
A: LogFC and LogCPM
Comment: Help with running egsea()
removeBatchEffect explained using base R linear models
Comment: Help with running egsea()
Why employ normalization methods, and how can they be utilized in DEG analysis?
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Recent Replies
Comment: UMI-Tools knee-method has great influence on the results of white list
by
i.sudbery
19k
I can't immediately see anything wrong. The log file should contain lines saying how many reads were parsed, how many reads matched the bar…
Comment: UMI-Tools knee-method has great influence on the results of white list
by
Assa Yeroslaviz
★ 1.8k
Thank you for the explanation. I can see the plots look strange, but i truly don't know why this is. I have a feeling that the sequencing …
Comment: High Malat-1 expression in single cell data
by
dsull
★ 6.0k
No -- those are ribosomal proteins, not rRNAs.
Comment: trying to count a pattern in my fastq file using bbduk
by
GenoMax
142k
Thanks for that link. As noted in that example, you can try `seal.sh` instead of `bbduk.sh`. > Is it possible, that this pattern is just …
Comment: Question regarding WGCNA
by
deepak
• 0
These are independent biological replicates
Comment: UMI-Tools knee-method has great influence on the results of white list
by
i.sudbery
19k
I didn't mean to sound like I was taking it as a criticism, I genuinely meant that we never intended to be a foolproof whitelisting tool. T…
Comment: Help with running egsea()
by
Chris
▴ 270
Thanks 1769mkc! I also tried fgsea. The author of limma comment on this post that p value from fgsea is not truly significant as it is http…
Comment: trying to count a pattern in my fastq file using bbduk
by
Assa Yeroslaviz
★ 1.8k
yes it does. As far as I understand it, you can use `N` here. I took it from [this example][1] Brian posted a few years ago This is why…
Comment: UMI-Tools knee-method has great influence on the results of white list
by
Assa Yeroslaviz
★ 1.8k
thanks for the answer. I wasn't complaining about the tool (or the results for that matter). I'm just trying to understand why the differe…
Comment: Help with running egsea()
by
1769mkc
★ 1.2k
"c2 gene set from MSigDB." this i agree in that case https://bioconductor.org/packages/release/bioc/html/fgsea.html you can try this one wh…
Comment: UMI-Tools knee-method has great influence on the results of white list
by
i.sudbery
19k
If you can post the knee plot, that might be helpful. But I will add that the whitelist command in UMI-tools was primarily designed to be a…
Comment: Help with running egsea()
by
Chris
▴ 270
Thanks 1769mkc! I tried this tool. Gene expression of 2 groups is just slightly different (not hundred of differential express genes). The …
Comment: Help with running egsea()
by
1769mkc
★ 1.2k
https://metascape.org/ this is one of the ways to make life easier if you have the genes already from the differential list
Comment: RNA editing sites based on DNA seq and RNA seq
by
Ahiad Chen Zion
• 0
In those unaligned reads, I am looking for hyper-editing. But the alignment should be much higher
Comment: Bacterial plasmid analysis
by
GenoMax
142k
Once you have some of these basic issues sorted out you can create a `tools` post describing `pling`.
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