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
357 results • Page
2 of 8
Sort: Views
Rank
Views
Votes
Replies
1
vote
14
replies
612
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
9 hours ago by
hophuquy0944
• 0
0
votes
0
replies
607
views
Differential accessibility using DiffBinf
diffbind
18 days ago by
Shloka
• 0
0
votes
1
reply
606
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 15 days ago by
mdav
• 0 • written 19 months ago by
Zoe
• 0
0
votes
9
replies
598
views
Using VEP annotation output as the input for a second VEP annotation
Annotation
VEP
VCF
1 day ago by
Arton
▴ 10
3
votes
8
replies
597
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
10 days ago by
Qroid
▴ 40
0
votes
2
replies
596
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
28 days ago by
航太郎
• 0
0
votes
2
replies
589
views
autodockvina
python
python3
autodock
updated 28 days ago by
Ram
43k • written 4 months ago by
iamsmor
• 0
0
votes
0
replies
586
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
20 days ago by
biocellbio
• 0
0
votes
4
replies
581
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
29 days ago by
feather-W
• 0
1
vote
0
replies
561
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers
TRINITY
27 days ago by
mathavanbioinfo
▴ 90
0
votes
1
reply
560
views
HOMER on AWS
HOMER
updated 14 days ago by
clairechung112
• 0 • written 2.3 years ago by
Bogdan
★ 1.4k
3
votes
3
replies
551
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 27 days ago by
swbarnes2
14k • written 28 days ago by
noodle
▴ 580
1
vote
8
replies
543
views
Downsampling fastq file
downsample
fastq
16 days ago by
marco.barr
▴ 130
1
vote
7
replies
536
views
Question regarding WGCNA
WGCNA
Network-construction
8 days ago by
deepak
• 0
0
votes
1
reply
536
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 22 days ago by
ginellegrenier
• 0 • written 5 months ago by
Clayton
• 0
2
votes
5
replies
535
views
Marking duplicates using UMIs
Deduplication
UMI
updated 25 days ago by
i.sudbery
19k • written 26 days ago by
Lipika
• 0
1
vote
1
reply
524
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
27 days ago by
renan.igor
• 0
1
vote
4
replies
499
views
cellranger error message
multiplexing
cellranger
updated 7 days ago by
Max
• 0 • written 3 months ago by
Alivia
▴ 10
0
votes
6
replies
496
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 23 days ago by
gv
• 0 • written 6 weeks ago by
Srinka
▴ 20
5
votes
7
replies
485
views
RNA seq analysis
DESeq
RNA-seq
2 days ago by
Jacek
▴ 20
0
votes
6
replies
474
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 13 days ago by
swbarnes2
14k • written 14 days ago by
Erina
• 0
0
votes
2
replies
471
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
28 days ago by
_quantum_girl_
▴ 10
0
votes
2
replies
462
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
28 days ago by
Ashok
• 0
0
votes
8
replies
459
views
Error in cnetplot enrichplot package
R
updated 24 days ago by
Ram
43k • written 24 days ago by
Farhad
• 0
0
votes
5
replies
458
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 20 days ago by
Istvan Albert
100k • written 23 days ago by
sehriban.buyukkilic
▴ 10
1
vote
1
reply
454
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 26 days ago by
Gordon Smyth
★ 7.2k • written 29 days ago by
Chris
▴ 280
1
vote
1
reply
452
views
ComBat_Seq stuck adjusting the data
Batch-Effect
RNAseq
ComBat-Seq
updated 8 days ago by
Jaïr
• 0 • written 4 months ago by
NorbertK
▴ 10
1
vote
3
replies
449
views
PCA plot
DESeq2
PCAplot
updated 18 days ago by
LauferVA
4.2k • written 22 days ago by
Aaliya
▴ 10
0
votes
5
replies
441
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 22 days ago by
GenoMax
142k • written 23 days ago by
Bertalan_Takacs
▴ 90
0
votes
2
replies
427
views
How can I solve this error?
metal
29 days ago by
22211020193
• 0
0
votes
5
replies
427
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
23 days ago by
njornet
▴ 20
0
votes
5
replies
424
views
Telescope issue
Telescope
RNA-seq
updated 15 days ago by
GenoMax
142k • written 16 days ago by
eleven11
• 0
0
votes
2
replies
420
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
28 days ago by
Ashok
• 0
0
votes
1
reply
418
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 29 days ago by
Ram
43k • written 20 months ago by
Muhammad
• 0
0
votes
4
replies
415
views
Highest variable features in single cell data
single-cell
10 days ago by
carolofharvest
▴ 40
1
vote
4
replies
412
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 6 days ago by
GenoMax
142k • written 29 days ago by
aniigodwinn
• 0
3
votes
7
replies
410
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
17 days ago by
salias
• 0
1
vote
6
replies
399
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 14 days ago by
GenoMax
142k • written 4 weeks ago by
eebloom
▴ 80
0
votes
4
replies
398
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
4 days ago by
beginner123
• 0
1
vote
9
replies
393
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 7 days ago by
i.sudbery
19k • written 10 days ago by
Assa Yeroslaviz
★ 1.8k
1
vote
3
replies
377
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 18 days ago by
ATpoint
82k • written 19 days ago by
Francesco
▴ 10
2
votes
4
replies
377
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
23 days ago by
samuelkalandarov2002
▴ 10
0
votes
2
replies
372
views
GSEA analysis in R
GSEA
R
Arabidopsis
29 days ago by
Sudip
• 0
0
votes
2
replies
365
views
How to update R on ubuntu
installation
update
R
apt-get
18 days ago by
Bosberg
▴ 50
0
votes
3
replies
362
views
CWl and toil singularity image e.g busybox? Thank you
toil
singularity
updated 18 days ago by
Ram
43k • written 5 months ago by
Fadi
• 0
1
vote
2
replies
358
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
ComBat-seq
limma
RNA-seq
removeBatchEffect
batch-effect
updated 4 days ago by
Ram
43k • written 4 days ago by
t.fortunato.asquini
• 0
1
vote
4
replies
343
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 2 days ago by
Juke34
8.6k • written 4 days ago by
Vijith
▴ 30
0
votes
3
replies
343
views
Snakemake wrapper issue
fastqc
snakemake
updated 3 days ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
2
votes
3
replies
337
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 7 days ago by
bk11
★ 2.5k • written 12 days ago by
Yoosef
▴ 60
2
votes
2
replies
334
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 22 days ago by
Ram
43k • written 23 days ago by
v.berriosfarias
▴ 140
357 results • Page
2 of 8
Recent Votes
differential gene expression analysis comparing different conditions using scRNAseq
Answer: Using Seurat function `FindMarkers` to find differentially expressed genes betwe
Looking for differential gene expression between treatment, within a specific cluster (seurat)
Comment: Details on salmon index
Course on Manual Genome Curation
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
Answer: Details on salmon index
Recent Locations •
All
The Netherlands,
2 minutes ago
France,
2 minutes ago
Belgium,
3 minutes ago
France/Nantes/Institut du Thorax - INSERM UMR1087,
5 minutes ago
United States,
7 minutes ago
India,
8 minutes ago
United States,
8 minutes ago
Recent Awards •
All
Scholar
to
Peter
6.0k
Popular Question
to
ashkan
▴ 160
Supporter
to
Umer
▴ 50
Scholar
to
zx8754
11k
Teacher
to
Rob
6.6k
Popular Question
to
Nyksubuz
▴ 20
Popular Question
to
Govardhan Anande
▴ 150
Recent Replies
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
Thank you. What exactly do you mean? Changing ha = rowAnnotation(text = anno_mark(at = mark_at, labels = gene_names_interesting_in_clusters…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
Ram
43k
Try tweaking the `gp` of the rowAnnotation instead of tweaking the `annotation_name_gp` - that might do the trick.
Comment: Help! Reconstruction of locus, order contigs
by
dthorbur
★ 2.0k
I don't understand your comment. What do you mean? > my idea is not to have to write it down If you have an alignment already, why can't…
Comment: Help! Reconstruction of locus, order contigs
by
GenoMax
142k
Please use `ADD REPLY/ADD COMMENT` when responding to existing content. `SUBMIT ANSWER` is for new answers to the original question.
Comment: Details on salmon index
by
Rob
6.6k
Hi Lorenzo, That is correct. The initial version of salmon used the RapMap index explained above. When we published the selective align…
Comment: Help! Reconstruction of locus, order contigs
by
BATMAN
• 0
Thanks for your reply, my idea is not to have to write it down. What I have is an alignment of the .gbk from the progressiveMauve. It would…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
Gabriel R.
★ 2.9k
I did some digging aroumd, no static binary. Plus it seems you need to roll your own program.
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
Gabriel R.
★ 2.9k
We tested it, however, it does not seem to produce a fast a file of the results or anything that we can easily parse. It produces a CIGAR a…
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@atpoint yes but for example for the kallisto results I have expression for 2080 genes (transcripts) and the rest are 0 but in my STAR resu…
Comment: In one PCA plot, can I calculate the percentage of different factors that contri
by
marco.barr
▴ 130
great team work! why can't you access and do the calculation for the other components too? can't you extract the information from the other…
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ATpoint
82k
Yes, but this is what I am saying: GAPDH in human has at least 6 annotated transcripts. Have you looked at all of them? Maybe that particul…
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@atpoint these are from PBMC. no they are different genes. for example ENST00000229239.10 is GAPDH. in STAR I got a lot of reads aligned …
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@dariober: I have to use kallisto for our downstream pipeline.
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ATpoint
82k
Which celltype is this? Are these transcripts of the same gene, and of which gene?
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@atpoint the question is updated. the first command shows how the index is built.
Traffic: 2768 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