Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this month
all time
today
this week
this month
this year
498 results • Page
4 of 10
Sort: Views
Rank
Views
Votes
Replies
0
votes
6
replies
445
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 5 days ago by
gv
• 0 • written 28 days ago by
Srinka
▴ 20
0
votes
2
replies
428
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
10 days ago by
_quantum_girl_
▴ 10
1
vote
1
reply
422
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 8 days ago by
Gordon Smyth
★ 7.0k • written 11 days ago by
Chris
▴ 260
0
votes
2
replies
420
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
10 days ago by
Ashok
• 0
1
vote
1
reply
416
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
10 days ago by
renan.igor
• 0
1
vote
1
reply
416
views
Long reads Annotation
long-reads
pacbio
updated 23 days ago by
Ram
43k • written 2.1 years ago by
Gerardo
• 0
0
votes
0
replies
415
views
Pairwise alignment of two long chromosomes (~100Mbp) with lastz
lastz
alignment
updated 23 days ago by
Ram
43k • written 21 months ago by
vahe.galstyan
• 0
2
votes
6
replies
413
views
create a gene count matrix csv file from seurat object
Seurat
sparseMatrix
20 days ago by
jkim
▴ 170
0
votes
7
replies
412
views
DESeq: too low p-value for RNAseq
R
DESeq
p-value
RNA-seq
FDR
updated 24 days ago by
Papyrus
★ 2.9k • written 25 days ago by
doramora
▴ 10
0
votes
5
replies
407
views
Used featureCounts to generate a count matrix for sc RNA-seq and it has all 0s.
scRNA-seq
updated 19 days ago by
GenoMax
141k • written 20 days ago by
Shay
• 0
2
votes
4
replies
405
views
Per Base Sequence Content - continuous raise of G%
fastqc
updated 19 days ago by
GenoMax
141k • written 20 days ago by
pl.terzian
• 0
5
votes
6
replies
403
views
7 follow
Seeking Help with Unexpected MA Plot Output
MAplot
RNAseq
Rstudio
updated 27 days ago by
Istvan Albert
100k • written 27 days ago by
Pumla
• 0
0
votes
1
reply
403
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 11 days ago by
Ram
43k • written 19 months ago by
Muhammad
• 0
0
votes
0
replies
400
views
BETA whether on the same scale when performing rank-based inverse normal transformation on the same type of phenotype data for two cohorts separately…
normal
inverse
transformation
18 days ago by
Isaac
• 0
1
vote
4
replies
399
views
what is the normal range of htseq-count output for homo sapiens RNA-Seq
Transcriptomics
htseq-count
RNA-Seq
NGS
hisat2
updated 16 days ago by
BioinfGuru
★ 1.7k • written 17 days ago by
Morteza
• 0
1
vote
3
replies
398
views
multiple sequence alignment
BLAST
multiple-sequence-alignment
clustal-omega
MSA
updated 20 days ago by
Ram
43k • written 23 days ago by
catherinemaria2728
• 0
0
votes
2
replies
382
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
10 days ago by
Ashok
• 0
0
votes
0
replies
380
views
Realistic RNA-seq using Polyester + Differences between Hexamer bias and positional bias?
polyester
short-read
bias
updated 27 days ago by
Ram
43k • written 18 months ago by
shinyjj
▴ 50
0
votes
2
replies
379
views
How can I solve this error?
metal
11 days ago by
22211020193
• 0
0
votes
2
replies
376
views
I can't add VAF from population for all of my variants from VCF file
vaf
vcf
genomics
gnomad
allelicfrequency
29 days ago by
Samuel
▴ 20
0
votes
0
replies
375
views
The chromatin accessibility in regulatory regions of the rhodopsin gene RHO.
ATAC-Seq
updated 27 days ago by
Ram
43k • written 2.7 years ago by
madhubioinform
• 0
1
vote
4
replies
372
views
Molecular docking with Autodock
Docking
proteomics
updated 24 days ago by
Ram
43k • written 12 weeks ago by
shwetamgr1
▴ 10
4
votes
4
replies
371
views
Average expression of a sample in single-cell data
single-cell
rna-seq
27 days ago by
newuser2024
• 0
1
vote
0
replies
368
views
Differential expression analysis on multiple integrated datasets
microarray
Z-score
limma
differential-gene-expression
meta-analysis
updated 20 days ago by
Ram
43k • written 2.4 years ago by
michael.s
▴ 10
3
votes
4
replies
364
views
Single cell analysis with "meta".tsv.gz file
Single-cell
26 days ago by
Estevão
• 0
1
vote
3
replies
362
views
Ensembl gene id conversion
biomart
ensembl
updated 13 days ago by
ATpoint
82k • written 15 days ago by
naveedhasan2000
• 0
0
votes
0
replies
357
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer
ATAC-seq
12 days ago by
Ronin
• 0
1
vote
3
replies
355
views
how to do the repeatability filtering of vcf files?
snp
vcf.
updated 27 days ago by
Pierre Lindenbaum
161k • written 29 days ago by
Max
• 0
1
vote
5
replies
349
views
samtools filtering
samtools
updated 18 days ago by
jkbonfield
★ 1.2k • written 25 days ago by
sansan_96
▴ 80
1
vote
4
replies
348
views
How to get human-mouse conservation score from UCSC
conservation
mouse
IGV
human
score
24 days ago by
diqixiaoyaoer
▴ 10
0
votes
3
replies
345
views
Resources regarding Proteomics (In-Silico)
molecular-simulation
docking
protein
proteomics
updated 27 days ago by
Ram
43k • written 5 weeks ago by
Saurabh
• 0
0
votes
4
replies
344
views
What is the samtools flag used in bamPEFragment?
deeptools
updated 18 days ago by
GenoMax
141k • written 20 days ago by
Soohyun
• 0
0
votes
4
replies
343
views
Compute bootstrap values on consensus tree
phylogeny
tree
raxml
14 days ago by
pablo
▴ 300
0
votes
5
replies
342
views
Incongruencies in GT assignment by Freebayes
depth
freebayes
heterozygous
genotype
24 days ago by
virginia.baraja
• 0
1
vote
7
replies
341
views
Downsampling fastq file
downsample
fastq
updated 1 hour ago by
Ram
43k • written 7 days ago by
marco.barr
▴ 80
0
votes
7
replies
340
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 3 days ago by
GenoMax
141k • written 7 days ago by
Patadu94
• 0
0
votes
5
replies
340
views
BUSCO analysis failed due to Duplicate of sequence in Input genome fasta. How to solve this problem ?
duplicate
BUSCO.
updated 24 days ago by
GenoMax
141k • written 25 days ago by
Sony
▴ 10
0
votes
8
replies
339
views
Error in cnetplot enrichplot package
R
updated 6 days ago by
Ram
43k • written 6 days ago by
Farhad
• 0
3
votes
3
replies
339
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio
volcano-plot
29 days ago by
Pumla
• 0
0
votes
0
replies
338
views
Looking to improve my understanding of Homer's mergePeaks function: unclear of how the merged file is created?
Homer
ATACseq
25 days ago by
Ronin
• 0
1
vote
2
replies
337
views
BAM to CRAM and BAM recover with smaller size
BAM
samtools
CRAM
updated 26 days ago by
jkbonfield
★ 1.2k • written 6 weeks ago by
geocarvalho
▴ 360
1
vote
3
replies
336
views
PCA plot
DESeq2
PCAplot
updated 22 hours ago by
LauferVA
4.2k • written 4 days ago by
Aaliya
▴ 10
0
votes
5
replies
336
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 4 days ago by
GenoMax
141k • written 5 days ago by
Bertalan_Takacs
▴ 90
0
votes
2
replies
335
views
Why are gene models from JGI non-sense when using AGAT to to extract proteins?
translation
models
gif
gene
cgi
27 days ago by
O.rka
▴ 710
0
votes
5
replies
333
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 2 days ago by
Istvan Albert
100k • written 5 days ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
330
views
How to convert dataframe properly to anndata?
single-cell
python
anndata
updated 24 days ago by
Ram
43k • written 6 months ago by
bioinfo
▴ 150
2
votes
4
replies
329
views
SnpEff annotates coding duplication as intronic?
snpeff
12 days ago by
kirill.zaslavsky
• 0
0
votes
0
replies
328
views
GTEx long read data
short-read
long-read
gtex
updated 23 days ago by
Ram
43k • written 19 months ago by
shinyjj
▴ 50
0
votes
2
replies
327
views
GSEA analysis in R
GSEA
R
Arabidopsis
11 days ago by
Sudip
• 0
0
votes
0
replies
327
views
How to import filtered_tf_bc_matrix and add it to my anndata object?
python
anndata
atac-seq
updated 24 days ago by
Ram
43k • written 6 months ago by
bioinfo
▴ 150
498 results • Page
4 of 10
Recent Votes
Difference between Genotype 0|1 and 1|0 in VCF file?
Answer: Mapping ortholog human and mouse transcript
C: Kallisto missing Bootstrap
Answer: Very low RNA splicing rate for pulmonary AT2 cells
Answer: what is the purpose of indexing the reference genome (Kallisto)
The Biostar Herald for Monday, April 29, 2024
The Biostar Herald for Monday, April 29, 2024
Recent Locations •
All
Sweden,
just now
United Kingdom,
just now
Turkey,
just now
United States,
2 minutes ago
United States,
2 minutes ago
France,
3 minutes ago
Spain,
3 minutes ago
Recent Awards •
All
Scholar
to
e.r.zakiev
▴ 200
Popular Question
to
Bine
▴ 60
Popular Question
to
Deepak Tanwar
★ 4.2k
Popular Question
to
Chris
▴ 260
Popular Question
to
Trivas
★ 1.7k
Popular Question
to
noodle
▴ 570
Popular Question
to
SaltedPork
▴ 170
Recent Replies
Comment: When to use .vcf or .gvcf files from GATK HaplotypeCaller?
by
Medhat
9.7k
"./." in your gVCF files typically indicates a lack of information or uncertainty about the genotype at that particular position. This co…
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt
by
salias
• 0
Fungal ITS2 region (length is really variable so read-through can be an issue)
Answer: Is it possible to bulk download files from GEO repository?
by
noodle
▴ 570
Also try the NCBI AWS bucket transfer tool. It's extremely convenient, however it's not instantaneous and you need to have a (paid) AWS acc…
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt
by
GenoMax
141k
Check a random sampling of reads to make sure the adapters are being removed. You may also want to blast a few reads to ensure that there i…
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt
by
salias
• 0
Many thanks for your comment. If read-through is happening, shouldn't Cutadapt being taking care of that there? I provided to the Cutadapt …
Comment: How should I make kallisto indexes?
by
bioinfo
▴ 150
Thank you. I will read the documentation you attached. Are you going to slowly phase out the not kb ref commands? Also, does the t2g.txt fi…
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt
by
GenoMax
141k
> I need to understand why is this happening More than likely you have library fragments that are shorter than the length of sequencing. W…
Comment: Genbank File Format
by
Mensur Dlakic
★ 27k
I think this is a question for CLC support. It should be trivial for them to combine these fields into one. In other words, you need a bett…
Answer: Programmatically retrieving positions of protein active site residues
by
Mensur Dlakic
★ 27k
Although this probably doesn't qualify as `programmatically retrieving positions`, you can always do it by sequence alignments. This can be…
Answer: metagenomic virome quality assessment
by
Mensur Dlakic
★ 27k
The error message points to a problem with `prodigal-gv`. What happens when you type `prodigal-gv` on the command line? It is never a go…
Comment: Programmatically retrieving positions of protein active site residues
by
Wayne
★ 2.0k
"I have seen other similar posts but a lot of the tools and websites suggested are down." Please show & share your research as part of you…
Comment: Software to separate reads from different individuals
by
njornet
▴ 20
No... the extracted sample is already a mix so no way to barcode
Comment: Very low RNA splicing rate for pulmonary AT2 cells
by
e.r.zakiev
▴ 200
For anyone it might be useful: a colleague of mine, who was not dumb to use the wrong annotation `gtf` as I did, also observed an important…
Answer: Very low RNA splicing rate for pulmonary AT2 cells
by
e.r.zakiev
▴ 200
Hello people sorry I am dumb the problem lied in the fact that I had mouse cells but my `.gtf` transcriptome file was for the human. Now wi…
Comment: Genbank File Format
by
GenoMax
141k
Can you indicate if you need to do this within CLC or can use an external solution (if someone provides it here). If you need to do this in…
Traffic: 2829 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6