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236 results • Page
2 of 5
Sort: Rank
Rank
Views
Votes
Replies
0
votes
2
replies
164
views
novel and know mir156 and mir172
a
updated 1 day ago by
gayachit
▴ 200 • written 1 day ago by
Fadmo
• 0
0
votes
1
reply
107
views
Update R in Posit Workbench
R
Posit
updated 1 day ago by
Ram
43k • written 1 day ago by
Nitin
• 0
2
votes
8
replies
261
views
Piping samtools to R
R
NGS
bash
samtools
1 day ago by
joe
▴ 470
8
votes
6
replies
400
views
Pangenome of plant
pangenome
plant
updated 1 day ago by
talbots
• 0 • written 2 days ago by
analyst
▴ 10
1
vote
2
replies
186
views
vg call is time consuming
vg
1 day ago by
Maxine
▴ 40
4
votes
14
replies
4.5k
views
8 follow
Installation: Tax4Fun2 package are not found and github repository is not maintained anymore
Tax4Fun2
updated 1 day ago by
Ram
43k • written 21 months ago by
Elsa
▴ 20
0
votes
8
replies
419
views
STAR aligner options
STAR
19 hours ago by
theophile
• 0
2
votes
3
replies
511
views
Website or tool to obtain a list of genes that participate in a specific process?
genomics
updated 1 day ago by
NancyTLi
• 0 • written 3 months ago by
Hamtaro
▴ 50
0
votes
2
replies
299
views
How to obtain Node/ Edge information from a Reactome Pathway
R
API
pathways
reactome
databases
updated 1 day ago by
GenoMax
140k • written 4 weeks ago by
K.patel5
▴ 140
0
votes
2
replies
164
views
Why counting by diffbind and featurecounts differ?
featurecounts
diffbind
1 day ago by
Ankit
▴ 500
0
votes
1
reply
106
views
Wanting to make a Venn diagram of ATACseq peak files, unsure of where to start
ATAC-seq
updated 1 day ago by
Yogi
▴ 70 • written 1 day ago by
Ronin
• 0
0
votes
0
replies
81
views
Association Module to traits
module-trait-relationships
WGCNA
GENIE3
DOMINO
updated 1 day ago by
Ram
43k • written 1 day ago by
r.shiasi3897
▴ 10
0
votes
0
replies
84
views
Number of pathway result from GSVA
GSVA
1 day ago by
Chris
▴ 260
0
votes
1
reply
123
views
How can I remove duplicate SNP?
plink
updated 1 day ago by
iraun
6.2k • written 1 day ago by
Zhennan
• 0
0
votes
1
reply
132
views
SNP VCF files from hybrid populations and parental populations generated by GBS in public databases
contaminations
verification
parental
check
updated 1 day ago by
Ram
43k • written 1 day ago by
Hajar
• 0
0
votes
0
replies
77
views
Creating a custom ontology for peptides
ontology
peptide
1 day ago by
Mathew
• 0
0
votes
3
replies
223
views
convert cds to seurat object
R
monocle3
seurat
updated 18 hours ago by
edoardofilippi1998
• 0 • written 1 day ago by
sooni
▴ 20
0
votes
0
replies
79
views
GSEA number dimension of expression dataset
GSEA
1 day ago by
edoardofilippi1998
• 0
0
votes
2
replies
217
views
Limma compare between 3 conditions vs 2 conditions
Limma
1 day ago by
Chris
▴ 260
0
votes
0
replies
85
views
single cell data integration approach
comparison
integration
pairwise
singlecell
1 day ago by
Jay
• 0
0
votes
3
replies
217
views
High number of detected genes per cell after doublet removal - scRNAseq data
scRNAseq
duoblet
1 day ago by
sarahmanderni
▴ 100
1
vote
1
reply
205
views
DESeq2 and normalization
RNA-seq
normalization
DESeq2
updated 1 day ago by
GenoMax
140k • written 2 days ago by
JH
• 0
0
votes
2
replies
155
views
Error with goodSamplesGenes()
R
WGCNA
1 day ago by
bioinfo_enthusiast
• 0
0
votes
0
replies
92
views
Variant Enrichment Analysis
Analysis
Enrichment
VEP
Variant
1 day ago by
Mojtaba
• 0
0
votes
7
replies
320
views
Salmon Quantification in Alignment based-mode
Salmon
RNA-seq
TPM
updated 1 day ago by
GenoMax
140k • written 1 day ago by
Patadu94
• 0
0
votes
1
reply
145
views
dbsnp flanks information
dbsnp
updated 1 day ago by
Pierre Lindenbaum
160k • written 1 day ago by
sskimvd
• 0
0
votes
1
reply
142
views
Cell communacations analysis. I only have the proteome of one type of cell
How
to
updated 1 day ago by
ATpoint
81k • written 2 days ago by
David Arturo
• 0
0
votes
0
replies
104
views
bulk RNA-seq: how to remove batch effect between multiple batches and labels?
combat
batch
2 days ago by
kiraqueen
• 0
2
votes
2
replies
214
views
A pipeline for prediction and annotation of obelisks
rna-seq
updated 1 day ago by
Pierre Lindenbaum
160k • written 2 days ago by
fred.s.kremer
▴ 110
6
votes
12
replies
5.5k
views
6 follow
Getting sample information from GEO
GEO
NCBI
updated 2 days ago by
Tania
• 0 • written 6.9 years ago by
Tom_L
▴ 350
0
votes
0
replies
103
views
Convert VCF file and add covariate information
VCF
PED
PLINK
2 days ago by
asmariyaz23
▴ 10
0
votes
0
replies
103
views
Merging Hi-C datasets originating from experiments using different enzymes
enzymes
Hi-C
updated 2 days ago by
Ram
43k • written 2 days ago by
hamarillo
▴ 70
0
votes
2
replies
217
views
Using the Ontology Lookup Service (OLS) API
API
OLS
1 day ago by
longoka
▴ 40
7
votes
2
replies
202
views
Create a new reference genome with denovo assembly and standard reference with long read data?
PacBio
updated 2 days ago by
gconcepcion
▴ 410 • written 2 days ago by
eorr
▴ 30
2
votes
3
replies
242
views
Extracting information from my VCF file
VCF
updated 2 days ago by
bioruffo
▴ 40 • written 2 days ago by
realtreeecat
• 0
0
votes
4
replies
244
views
Coverage observed in introns in the Knockdown genes but not in knockout genes
RNA-seq
STAR
IGV
17 hours ago by
rohitsatyam102
▴ 840
0
votes
2
replies
270
views
JASPAR2024_getMatrixSet error
getMatrixSet
JASPAR2024
updated 2 days ago by
Ram
43k • written 5 weeks ago by
maplewj
▴ 10
2
votes
3
replies
471
views
Should I use Dfam or a custom repetitve elements library (from PlantRep) as a repeat database; using RepeatMasker in a Linux machine?
genome
sequence
repeatmasker
blast
updated 1 day ago by
b.contreras.moreira
▴ 70 • written 2 days ago by
Vijith
▴ 30
0
votes
0
replies
92
views
How to access an image (slice) of interest in spatial analysis
spatial-transcriptomics
Seurat
Visium
updated 2 days ago by
Ram
43k • written 2 days ago by
piotto
▴ 20
0
votes
2
replies
184
views
Fpkm and log2fold change and pcr validation
fpkm
updated 2 days ago by
bioruffo
▴ 40 • written 2 days ago by
mounavisirekolam
• 0
2
votes
2
replies
202
views
Location of NCBI ftp site changed?
ftp
ncbi
2 days ago by
sampsa.hyvamaki
• 0
0
votes
1
reply
162
views
MACS3 or SEACR
MACS3
SEACR
updated 2 days ago by
jared.andrews07
★ 16k • written 2 days ago by
daffodil
▴ 10
0
votes
0
replies
115
views
Visium dataset distance between spots calculations
SpatialSeq
Visium
updated 2 days ago by
GenoMax
140k • written 2 days ago by
houssi301
• 0
0
votes
0
replies
98
views
Best codeml model for estimating omega, M0 ?
codeml
ete3
evol
2 days ago by
Adrian Pelin
★ 2.6k
1
vote
1
reply
154
views
Pool-Seq same as normal variant calling?
Pool-Seq
Variant-Calling
updated 2 days ago by
dthorbur
★ 1.7k • written 2 days ago by
andrebolerbarros
• 0
0
votes
1
reply
148
views
Karytotype color annotations
karyotype
annotations
chromosome
color
updated 2 days ago by
Pierre Lindenbaum
160k • written 2 days ago by
Mary
• 0
0
votes
1
reply
224
views
What alternative method would recommend for conducting gene ontology analysis?
WEGO
gene-ontology
updated 2 days ago by
dthorbur
★ 1.7k • written 3 days ago by
mathavanbioinfo
▴ 80
1
vote
12
replies
543
views
Nanopore data filtering using fastp
fastp
nanopore
13 hours ago by
emilydolivo97
• 0
1
vote
2
replies
221
views
Is it possible to see so little adipocyte in white adipose tissue?
scRNA-seq
1 day ago by
kayah
• 0
2
votes
2
replies
229
views
singlecell annotation
scRNA-seq
annotation
1 day ago by
kayah
• 0
236 results • Page
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Recent Votes
Synthetic lethality and cancer database
Answer: log2(TPM+1)
Comment: Error in openning FastQC
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
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Pierre Lindenbaum
160k
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brian.fristensky
▴ 460
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★ 2.4k
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104k
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Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Yikes. Well, this is from an Illumina MiniSeq. Sure, I will use alignment, but only to remove host reads. Then the remaining reads will go …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
This is going to be tough to diagnose. Are you going to align to a reference? If so go ahead with the alignments to see if alignments turn …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Thank you for replying. I have separated the reads with at least one N on them and they account for 0.2% of the total reads in the file (8'…
Comment: Error running local blastn in R using system2
by
Mensur Dlakic
★ 26k
The `-db data/nt_euk` switch means that in your current directory you have a subdirectory called `data`, and all the `nt_euk` files are in …
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Thank you for your opinion. I will try with lower LEADING and TRAILING bases. By the way, I tried to set `keepBothReads:true` through sear…
Comment: Error in openning FastQC
by
GenoMax
140k
At this point it would be beneficial to learn some of the basics of command line. Please use this UNIX tutorial since you seem to be new to…
Comment: vcf file: number of samples does not match number of columns
by
Pierre Lindenbaum
160k
> ore or have any suggestions for fixing it? it's a problem with your upstream process. You'd better fix it.
Comment: Error in openning FastQC
by
friszd
• 0
after running fastqc -o output.html input.fastq, terminal returns: " Specified output directory 'output.html' does not exist " , when i run…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
The question you should be looking into is why the Q scores are dropping there? Are there `N` calls indicating some issue with that cycle?
Comment: Error in openning FastQC
by
GenoMax
140k
What is `ctrl+c ctrl+v`? You may actually be killing the running fastqc process. If you run `fastqc` interactively (like what was shown ab…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Dave Carlson
★ 1.7k
Ugh. I've definitely done this one before as well. And was none too happy about it.
Comment: Error in openning FastQC
by
friszd
• 0
fastqc -o output.html input.fastq ctrl+c ctrl+v
Comment: Error running local blastn in R using system2
by
GenoMax
140k
What do you see if you `cat nt_euk.nal`? Do the number of pieces mentioned in that file match with what you locally have?
Comment: Low number of both surviving reads after trimming
by
GenoMax
140k
It is your data and if you want to do that it is up to you. You may be throwing away essentially good data (you should remove the nextera s…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Istvan Albert
100k
Some things never change ... the most common mistake is still the one on top there
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