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190 results • Page
2 of 4
Sort: replies
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Views
Votes
Replies
1
vote
4
replies
1.0k
views
Filtering qscore on dorado
dorado
filtering
QC
nanopore
Guppy
2 days ago by
eebloom
▴ 80
0
votes
4
replies
258
views
Genbank File Format
gbkformat
4 days ago by
alenew.am
• 0
0
votes
3
replies
216
views
Software to separate reads from different individuals
software
development
nanopore
updated 4 days ago by
GenoMax
142k • written 5 days ago by
njornet
▴ 20
2
votes
3
replies
207
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 23 hours ago by
dthorbur
★ 1.9k • written 1 day ago by
Vijith
▴ 30
0
votes
3
replies
336
views
CWl and toil singularity image e.g busybox? Thank you
toil
singularity
updated 4 days ago by
Ram
43k • written 4 months ago by
Fadi
• 0
1
vote
3
replies
302
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 5 days ago by
ATpoint
82k • written 6 days ago by
Francesco
▴ 10
0
votes
3
replies
739
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 4 days ago by
weidonglu
• 0 • written 21 months ago by
JZX
• 0
1
vote
3
replies
192
views
DiffBind: no peaks in DBA
MACS2
DiffBind
ChIP-seq
updated 1 day ago by
jared.andrews07
★ 16k • written 1 day ago by
yvonneh
▴ 10
1
vote
3
replies
219
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ
RNAseq
updated 1 day ago by
ATpoint
82k • written 1 day ago by
Qi
• 0
0
votes
3
replies
389
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
3 days ago by
Assa Yeroslaviz
★ 1.8k
1
vote
3
replies
291
views
DESeq2 processing problems
deseq2
R
updated 2 days ago by
ATpoint
82k • written 3 days ago by
jagdish7921
• 0
3
votes
3
replies
297
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 1 day ago by
ATpoint
82k • written 2 days ago by
alifafiq1
• 0
5
votes
3
replies
270
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 4 days ago by
Lluís R.
★ 1.2k • written 4 days ago by
이민경[학생](대학원 융합의과학과)
• 0
1
vote
3
replies
217
views
Odd alignment question/finding
Alignment
updated 1 day ago by
barslmn
★ 2.1k • written 2 days ago by
poordumbsillyidiot
• 0
0
votes
3
replies
280
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 4 days ago by
GenoMax
142k • written 4 days ago by
kim
• 0
1
vote
3
replies
385
views
PCA plot
DESeq2
PCAplot
updated 5 days ago by
LauferVA
4.2k • written 9 days ago by
Aaliya
▴ 10
1
vote
3
replies
393
views
Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:1.1.1.4, 1.1.1.-, 1.1.1.303)?
ontology
metagenomics
database
enzymes
genomics
updated 5 days ago by
Mensur Dlakic
★ 27k • written 7 days ago by
O.rka
▴ 710
1
vote
3
replies
273
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 3 days ago by
GenoMax
142k • written 3 days ago by
jeffrey.maurer.informatics
• 0
0
votes
3
replies
275
views
KEGG Pathways
r
RNA-seq
updated 3 days ago by
Ram
43k • written 4 days ago by
Sudip
• 0
4
votes
3
replies
367
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 6 days ago by
Arup Ghosh
3.2k • written 7 days ago by
chaco001
▴ 40
1
vote
3
replies
205
views
Bedtools merge minimum overlap?
bedtools
genomics
updated 1 day ago by
Alex Reynolds
35k • written 1 day ago by
SJP
• 0
3
votes
3
replies
323
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 4 days ago by
noodle
▴ 580 • written 5 days ago by
WUSCHEL
▴ 750
3
votes
2
replies
376
views
Extract protein sequence
fasta
alignment
blast
3 days ago by
anna
▴ 20
3
votes
2
replies
298
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 5 days ago by
i.sudbery
19k • written 7 days ago by
vanbelj
▴ 40
1
vote
2
replies
338
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
6 days ago by
Francesco
▴ 10
1
vote
2
replies
240
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
2 days ago by
rianna.collins
• 0
0
votes
2
replies
686
views
homer not configured properly
Homer
makeTagDirectory
updated 1 day ago by
clairechung112
• 0 • written 23 months ago by
amahdi779
• 0
0
votes
2
replies
158
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
5 days ago by
Lluís R.
★ 1.2k
0
votes
2
replies
354
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 6 days ago by
Jesse
▴ 740 • written 9 days ago by
Broccoli
• 0
0
votes
2
replies
155
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
1 day ago by
dtnondorf
• 0
0
votes
2
replies
53
views
creating batch colum for batch correction
batch
correction
combat
1 hour ago by
Expert
▴ 10
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 20 hours ago by
e.r.zakiev
▴ 210 • written 3.8 years ago by
n.anuragsharma
▴ 40
0
votes
2
replies
223
views
How to update R on ubuntu
installation
update
R
apt-get
5 days ago by
Bosberg
▴ 50
0
votes
2
replies
132
views
Raw counts using stringtie
stringtie
RNA-seq
updated 22 hours ago by
GenoMax
142k • written 1 day ago by
ahmad.sajad4541
• 0
4
votes
2
replies
304
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
4 days ago by
pairedttest
▴ 10
0
votes
2
replies
202
views
What should I consider as FASTA for dataset?
PDB
FASTA
4 days ago by
Nafi
• 0
2
votes
2
replies
152
views
Analysis of intronic reads included scRNA-seq data
cell
single
updated 1 day ago by
t.montserrat.ayuso
▴ 10 • written 1 day ago by
carolofharvest
▴ 30
2
votes
2
replies
194
views
MA plot of shrunken fold change
MA-plot
Deseq2
updated 4 days ago by
ATpoint
82k • written 4 days ago by
Sudip
• 0
1
vote
2
replies
206
views
RNA-seq data for deep learning classification
rna-seq
1 day ago by
yahn
• 0
1
vote
2
replies
277
views
read length in structural variant calling
nanopore
SV
QC
ONT
variant
1 day ago by
eebloom
▴ 80
0
votes
2
replies
223
views
ERROR When Using Ensembl Plants Biomart Wget API
biomart
plant
ensembl
updated 3 days ago by
GenoMax
142k • written 4 days ago by
Dora
▴ 10
2
votes
2
replies
203
views
PDB related issue
rcsb
pdb
updated 5 days ago by
noodle
▴ 580 • written 5 days ago by
Nafi
• 0
1
vote
2
replies
224
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 3 days ago by
Ram
43k • written 4 days ago by
Ravita
• 0
0
votes
2
replies
152
views
Downloading older version of a tool
Alignment
tools
10 hours ago by
Ruqaiya
• 0
2
votes
2
replies
2.6k
views
Pindel Segmentation Fault Error
pindel
updated 3 hours ago by
Ruqaiya
• 0 • written 10.2 years ago by
Yuelin
▴ 20
2
votes
2
replies
264
views
p-value in CIBERSORT
CIBERSORT
p-value
3 days ago by
michelafrancesconi9
▴ 20
1
vote
2
replies
280
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
3 days ago by
Nafi
• 0
0
votes
1
reply
168
views
metagenomic virome quality assessment
viromics
metagenomics
updated 4 days ago by
Ram
43k • written 5 days ago by
Petchimuthu
• 0
0
votes
1
reply
335
views
absolute path for symbolic links in Snakefile
Snakemake
updated 6 days ago by
Jesse
▴ 740 • written 14 days ago by
yifangt86
▴ 60
0
votes
1
reply
750
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq
R
cellassign
batch-effect
updated 6 days ago by
Francesco
▴ 10 • written 3.3 years ago by
gt
▴ 30
190 results • Page
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Answer: RNA velocity for smart-seq2 dataset
Comment: Help with choosing a model species for Augustus for a de novo assembled genome.
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Comment: creating batch colum for batch correction
by
Expert
▴ 10
Thank you for your response. These samples were collected from the same patient at different time points(day 0, 8 and 18) and these are ind…
Comment: creating batch colum for batch correction
by
ATpoint
82k
Not sure I follow. Can you first of all describe which comparisons you want to make, pretending there was no batch effect at all. Write dow…
Comment: Pindel Segmentation Fault Error
by
Ruqaiya
• 0
This the tool still problematic?
Comment: Segmentation error while using a tool
by
Ruqaiya
• 0
Thank you for the advice, i'll keep that in mind.
Comment: Segmentation error while using a tool
by
Ruqaiya
• 0
I am trying to reproduce some bioinformatics data from a research paper-[this paper][1] as i was asked to work on an MRSA bioinfo project, …
Answer: Segmentation error while using a tool
by
Mensur Dlakic
★ 27k
Most likely you didn't do anything wrong. Going by your previous post that you have only 8 GB of RAM, the most likely reason is the lack of…
Comment: Segmentation error while using a tool
by
Thanujay S
• 0
Hey @Ruqaiya! Can you please give more details on why smalt is opted here? According to what I can see, the tool has become obsolete! Why …
Comment: Extracting mutation status from MAF files - TCGA
by
Thanujay S
• 0
Hey! Can you explain the question further? What have you tried?
Comment: Downloading older version of a tool
by
Ruqaiya
• 0
I tried the 2nd option only. I got the files of older version from the author but that version isn't working on my WSL, it's showing Segmen…
Comment: filtering before dada2
by
GenoMax
142k
> I encountered a significant decrease in the percentage of merged reads. You can check with `bbmerge.sh` from BBMap suite to see how many…
Comment: HCL database download
by
GenoMax
142k
Isn't the download link available above the plot: http://bis.zju.edu.cn/HCL/data/DGE/Adult-Transverse-Colon1_dge.txt.gz
Comment: fastq screen aligner no specified.
by
GenoMax
142k
You need to change this configuration file to point it to the location where the aligner executable can be found. So as an example followi…
Answer: Design matrix Differential expression analysis
by
Gordon Smyth
★ 7.1k
The expression levels do not change but the way that you have parametrized the expression levels does change. The two design matrices give…
Comment: The GDC Legacy Archive is retiring soon.
by
lcordeiro
▴ 40
Hi Zhenyu, do you happen to know how I can download metadata for some of the legacy files? I downloaded several IDATs from the legacy data …
Answer: Force PLINK2 to neglect chrX as the sex chromosome
by
chrchang523
10k
(cross-posted from https://groups.google.com/g/plink2-users/c/Qphx_6BpPII ) You need to use --chr-set, not --allow-extra-chr, to specify…
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