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507 results • Page
1 of 11
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Views
Votes
Replies
0
votes
0
replies
8
views
How to compare different illumina indices with each other to see how similar or different they are
alignment
sequencing
rna-seq
20 minutes ago by
Apex92
▴ 260
0
votes
0
replies
10
views
How to export ONE copy of unique sequence in Vsearch
blast
y
vsearch
taxono
uchime
updated 40 minutes ago by
andres.firrincieli
3.1k • written 43 minutes ago by
josc
• 0
0
votes
0
replies
14
views
geom_errorbar not dodging or producing horizontal line
ggplot2
geom_errorbar
53 minutes ago by
bsp017
▴ 40
1
vote
2
replies
29
views
Size of two scRNA-Seq conditions
scRNA-Seq
14 minutes ago by
Chris
▴ 60
0
votes
0
replies
26
views
Mapping IDs to systematic names (GOSim, setevidencelevel() )
GOSim
updated 1 hour ago by
Ram
37k • written 3 hours ago by
eliska.ochodkova
• 0
0
votes
1
reply
55
views
Novogene somatic results with GATK mutect2
Mutect2
Novogene
GATK
somatic
VCF
updated 2 hours ago by
GenoMax
125k • written 4 hours ago by
chrisgr
▴ 20
2
votes
4
replies
103
views
fastqc: Per base sequence content
illumina
metagenomic
fastqc
updated 2 hours ago by
jv
▴ 790 • written 5 hours ago by
khoojj
• 0
0
votes
0
replies
56
views
A question about Bioinformatik analysis and experimental design / comparing 2 experiments
DEseq2
Batch-effect
updated 1 hour ago by
Ram
37k • written 5 hours ago by
Frederik
• 0
0
votes
0
replies
70
views
Input data for LIMMA: unnormalised or vsn or other?
lima
normalisation
vns
7 hours ago by
Sebastian Hesse
▴ 320
0
votes
0
replies
59
views
question of exonerate output
protein
gff
exonerate
annotation
9 hours ago by
TN
• 0
2
votes
0
replies
76
views
CircRNA extraction from bulk RNA seq datasets using CIRCexplorer2 with STAR alignment
alignment
CIRCexplorer2
STAR
9 hours ago by
choijamtsm
▴ 60
0
votes
0
replies
85
views
Mis-paired primers
amplicon
primers
Mis-paired
16 hours ago by
Sara
▴ 10
0
votes
0
replies
75
views
show amplicon like exon in UCSC/IGV
amplicon
17 hours ago by
Sara
▴ 10
0
votes
2
replies
147
views
scATAC-seq workflow
Signac
scATAC-seq
20 hours ago by
bioinformatics.girl
• 0
0
votes
0
replies
108
views
Set Y limits for ggplot with sec.axis
rstudio
ggplot
1 day ago by
JirMan
• 0
0
votes
0
replies
115
views
MetaboAnalyst: Interpreting Enrichment Analysis Results
enrichment
metabolomics
1 day ago by
eva_u
▴ 10
0
votes
1
reply
102
views
Filter InterProScan output for a specific function
interproscan
annotation
updated 1 hour ago by
jv
▴ 790 • written 1 day ago by
Purger
• 0
0
votes
1
reply
138
views
f-index in treemix
treemix
introgression
f-index
1 day ago by
kk.mahsa
▴ 140
0
votes
2
replies
282
views
Network analysis for two Factors
score
protein
network
chip-seq
analysis
1 day ago by
Ankit
▴ 390
0
votes
5
replies
362
views
ceres score in crispr screen
ceres
crispr
ngs
5 hours ago by
edus_bioinfo
▴ 20
0
votes
0
replies
189
views
Issues Using DMRcate and rmSNPandCH
DMRcate
R
1 hour ago by
Indira
• 0
0
votes
0
replies
138
views
Statistical test on two phylogenetically remote groups
phylogeny
ANOVA
1 day ago by
liorglic
★ 1.1k
0
votes
0
replies
169
views
Sequence Homology locator
Sequence
Homology
Genome
finder
2 days ago by
himalayan_yeti
• 0
0
votes
4
replies
288
views
How to find the most frequent alternative-splicing event from DEXSEQ data?
DESEQ
RNA-SEQ
DEXSEQ
1 hour ago by
STARDUST
• 0
1
vote
2
replies
268
views
SNP calling
SNP
GATK
updated just now by
dthorbur
▴ 260 • written 2 days ago by
abozorgmehr1985
▴ 10
0
votes
0
replies
171
views
gistic- overlapp
CNV
GISTIC
TCGA
2 days ago by
Hanie
• 0
0
votes
0
replies
188
views
Protocol to detect chromosomal ploidy from WGS VCF?
wgs
ploidy
2 days ago by
optimistsso4co3
▴ 100
0
votes
0
replies
174
views
SpliceAi same variant , different score
SpliceAi
updated 2 days ago by
Pierre Lindenbaum
152k • written 2 days ago by
vvasta
• 0
0
votes
1
reply
224
views
Diffbind losing peaks when going from small to larger consensus peak set
DiffBind
2 days ago by
tara.mcintyre
• 0
0
votes
0
replies
181
views
GSEA multiple group analysis
gsea
single-cell
2 days ago by
piotto
▴ 10
2
votes
6
replies
379
views
RNA Editing data from RNA-seq
Editing
RNA
2 hours ago by
Genetics
• 0
0
votes
2
replies
255
views
cellranger-arc mkfastq Error: bcl2fastq was killed with signal -11
bcl2fastq
cellranger-arc
mkfastq
cellranger
2 days ago by
Yingying
• 0
0
votes
0
replies
189
views
Unrooted consensus tree [Bio.Phylo]
consensus
phylo
biopython
2 days ago by
Jimpix
▴ 10
0
votes
6
replies
410
views
PLINK2 selecting variants based on INFO score
plink2
7 hours ago by
m.c.roozen
• 0
0
votes
0
replies
151
views
What is the difference between gseapy.prerank and gseapy.gsea?
gseapy
gsea
3 days ago by
bioinfo
▴ 20
3
votes
6
replies
337
views
Which file and data structure is used to create volcano plot from scRNA-Seq experiment?
plot
Volcano
2 days ago by
Chris
▴ 60
1
vote
1
reply
172
views
bwa mem duration?
performance
mapping
bwa
updated 3 days ago by
ATpoint
68k • written 3 days ago by
lacb
▴ 30
0
votes
1
reply
201
views
Gene ontology with locus tags
ontology
locus
gene
tags
updated 3 days ago by
dthorbur
▴ 260 • written 3 days ago by
sea.joson
▴ 10
0
votes
5
replies
283
views
Clustering and dynamic tree cutting
dynamicTreeCut
Clustering
data
RNAseq
cutreeDynamic
updated 4 hours ago by
andres.firrincieli
3.1k • written 3 days ago by
harish
• 0
0
votes
6
replies
326
views
STAR is running but .sam file size does not increase after hours mapping
STAR
RNA-seq
mapping
SAM
updated 3 days ago by
GenoMax
125k • written 3 days ago by
luzglongoria
▴ 40
0
votes
5
replies
442
views
HTSeq error processing GFF file
HTSeq
GFF
GTF
updated 2 days ago by
barslmn
★ 1.2k • written 3 days ago by
ibq.enriquepola
• 0
0
votes
0
replies
152
views
which tool to use for Transposon structure finding CENSOR or repeat masker ??
transposon
DNA
repeat
CENSOR
masker
3 days ago by
manaswiniparija3
▴ 10
0
votes
0
replies
152
views
scATAC merging of files
Signac
scATAC-seq
3 days ago by
bioinformatics.girl
• 0
0
votes
0
replies
161
views
what does ALT ID DUP refer to when ALT ID for copy number are already specified
ALT
ID
CNV
VCF
3 days ago by
anubratadas
▴ 20
0
votes
0
replies
181
views
How to use gseapy after scanpy?
gsea
single
cell
enrichR
gseapy
3 days ago by
bioinfo
▴ 20
0
votes
0
replies
159
views
VNTR genotyping
NGS
VNTR
genotyping
3 days ago by
Genotepes
▴ 950
0
votes
0
replies
125
views
Which AF column do I use from TCGA data in maftools
vcf2maf
sequencing
genome
WES
maf
3 days ago by
CH1374
▴ 10
0
votes
0
replies
127
views
Chloroplast genome phylogenetic analysis
Inverted
region
Chloroplast
genome
Phylogenetic
analysis
SSC
3 days ago by
a.bibek52
• 0
0
votes
0
replies
126
views
mVISTA annotation
alignment
Annotation
S-LAGAN
mVISTA
3 days ago by
a.bibek52
• 0
4
votes
2
replies
221
views
Analyzing bulk RNA-seq
RNAseq
updated 3 days ago by
swbarnes2
13k • written 3 days ago by
Zaid
• 0
507 results • Page
1 of 11
Recent Votes
Comment: fastqc: Per base sequence content
Comment: fastqc: Per base sequence content
Comment: Size of two scRNA-Seq conditions
Answer: Dealing with missing (NA) values in my 450K methylation array dataset
What type of database does gnomAD use?
What type of database does gnomAD use?
Answer: What type of database does gnomAD use?
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joe
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Matteo Schiavinato
★ 3.6k
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Recent Replies
Comment: Size of two scRNA-Seq conditions
by
Chris
▴ 60
Thank you so much for your answer! Here is the structure of 2 matrix objects of two conditions. Condition 1 has 19760 cells meanwhile condi…
Answer: Mapping with bbmap.sh
by
Mensur Dlakic
★ 22k
Definitely not normal. It doesn't seem that BBmap is taking any reads in. That's why your `num reads` and `num bases` are all zeros, which…
Comment: how to get an average ROC curve after 10-fold cross validation in r
by
Mensur Dlakic
★ 22k
I have no idea what cutoff is in this context, nor what you mean by `original` values. I don't know how you got those values for means. I …
Comment: Protein protein interactions
by
Mensur Dlakic
★ 22k
This is not a trivial calculation nor a simple sequence comparison like with BLAST, so it may take a while. Besides, there could be hundred…
Comment: snakemake Unexpected keyword bam in rule definition
by
Wayne
★ 1.6k
Any chance it is an indentation issue that isn't caused by what you aren't sharing here? See [here](https://groups.google.com/g/snakemake/c…
Comment: Size of two scRNA-Seq conditions
by
rpolicastro
11k
More important would be the cell QC stats (such as reads per cell and number of unique features detected per cell), the number of cells per…
Answer: What type of database does gnomAD use?
by
Jeremy Leipzig
21k
If you primarily want a variant warehouse that supports genomic region and sample queries at biobank scale, you should look into [TileDB-VC…
Answer: Dealing with missing (NA) values in my 450K methylation array dataset
by
Basti
★ 1.3k
You could omit the NA values : `pca <- prcomp(na.omit(t(exprs(GSE65820))))`
Comment: Virtual box
by
Ram
37k
This post does not fit the theme of this forum.
Comment: Filter InterProScan output for a specific function
by
jv
▴ 790
I imagine you can filter on things like E.C. numbers and domain names using `bash`, `awk`, `R`, or some other code.
Comment: How to find the most frequent alternative-splicing event from DEXSEQ data?
by
STARDUST
• 0
I will try both rMATS and SUPPA for categorising changes. For the specific exons, i'm expecting the last exons should be affected. That is …
Answer: snp Caenorhabditis elegans
by
GenoMax
125k
See: https://www.elegansvariation.org/data/release/20220216
Answer: want the codes for cuffdiff , NIOSeq , bayseq to perform DEGs.
by
jv
▴ 790
- NOISeq <https://www.bioconductor.org/packages/release/bioc/vignettes/NOISeq/inst/doc/NOISeq.pdf> - Cuffdiff <http://cole-trapnell-lab.gi…
Comment: fastqc: Per base sequence content
by
jv
▴ 790
I think this is to be expected based a report I was able to find online <https://uu.diva-portal.org/smash/get/diva2:1608120/FULLTEXT01.pd…
Comment: fastqc: Per base sequence content
by
GenoMax
125k
Unless the kit directions tell you to remove remove the initial 10-15 bp you may as well leave them alone. Data should align would be my in…
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