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 week
all time
today
this week
this month
this year
185 results • Page
2 of 4
Sort: Votes
Rank
Views
Votes
Replies
1
vote
2
replies
183
views
Duplicated sequence samtools
bowtie2
samtools
updated 5 days ago by
GenoMax
142k • written 5 days ago by
Moinuddin
• 0
1
vote
3
replies
439
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
5 days ago by
kalavattam
▴ 190
1
vote
4
replies
344
views
Contig assembly task, errors
dna
genetics
contig
assembly
updated 5 days ago by
Ram
43k • written 10 days ago by
samRayne
• 0
1
vote
2
replies
1.3k
views
Extracting named fasta sequences according to list with Biopython
Biopython
FASTA
updated 5 days ago by
Rubayetul
• 0 • written 2.6 years ago by
lachiemck
• 0
1
vote
1
reply
175
views
The total expressed genes in RNA-Seq data
RNA-SEQ
updated 4 days ago by
ATpoint
82k • written 5 days ago by
Pegasus
▴ 100
1
vote
2
replies
269
views
How to interpret infinite odds ratio?
statistics
4 days ago by
Lukas
• 0
1
vote
1
reply
147
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 4 days ago by
Ram
43k • written 4 days ago by
kilcdincer
▴ 10
1
vote
4
replies
350
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 4 days ago by
Juke34
8.6k • written 5 days ago by
Vijith
▴ 30
1
vote
2
replies
211
views
Alphafold 3 pLDDT coloring scheme in chimerax?
ChimeraX
Alphaphold
Alphaphold3
updated 3 days ago by
colindaven
6.4k • written 4 days ago by
mbrav005
• 0
1
vote
5
replies
221
views
Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
circos
atacseq
updated 3 days ago by
Pierre Lindenbaum
161k • written 3 days ago by
biology_inform
▴ 50
1
vote
3
replies
288
views
Using ggplotly in R
ggplot
ggplotly
updated 3 days ago by
jared.andrews07
★ 16k • written 4 days ago by
jen
▴ 10
1
vote
5
replies
800
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
1
vote
3
replies
208
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
updated 3 days ago by
Zhenyu Zhang
★ 1.2k • written 3 days ago by
shpak.max
▴ 50
1
vote
4
replies
291
views
Add stats to boxplot in R
stats
R
3 days ago by
Ghada
• 0
1
vote
2
replies
229
views
Doubt about the process of annotation, detection, identification and classification of transposable elements
annotation
TransposableElements
3 days ago by
MarcosCosta
• 0
1
vote
1
reply
247
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
3 days ago by
ramiro.barrantes
• 0
1
vote
4
replies
288
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
3 days ago by
Arton
▴ 10
1
vote
5
replies
266
views
Annotating file using bcftools
annotation
plink
bcftools
2 days ago by
kl
▴ 10
1
vote
1
reply
186
views
mitochondrial genome assembly pipeline
mammals
mitochondrial-genome
updated 2 days ago by
Ram
43k • written 2 days ago by
m90
▴ 30
1
vote
2
replies
229
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
2 days ago by
bioinfo
▴ 150
1
vote
3
replies
274
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 2 days ago by
GenoMax
142k • written 5 days ago by
ohtang7
▴ 40
1
vote
3
replies
801
views
About runing Pilon on individual chromosomes when polish draft genome assembly
Pilon
chromosome
polish
genome
draft
updated 2 days ago by
sansan_96
▴ 90 • written 2.7 years ago by
boymin2020
▴ 80
1
vote
1
reply
186
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 2 days ago by
Jordan M Eizenga
▴ 460 • written 12 days ago by
sarumonsus
▴ 10
1
vote
0
replies
131
views
News:
Course on Manual Genome Curation
Genome-Assembly
Pretext-View
Manual-Genome-Curation
updated 2 days ago by
Ram
43k • written 2 days ago by
carlopecoraro2
★ 2.5k
1
vote
1
reply
192
views
Tool:
Collect dispersed executable files and run them by using bingo.
bingo
updated 2 days ago by
Ram
43k • written 3 days ago by
dwpeng
▴ 10
1
vote
3
replies
272
views
Tool:
Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes
Decimal
offtopic
Degrees
python
updated 2 days ago by
Ram
43k • written 3 days ago by
kuttibiotech2009
▴ 30
1
vote
1
reply
181
views
API kegg - IndexError: list index out of range
kegg
API
updated 2 days ago by
Nyksubuz
▴ 20 • written 2 days ago by
mirwa.zidi93
• 0
1
vote
5
replies
319
views
Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 1 day ago by
dthorbur
★ 2.0k • written 2 days ago by
BATMAN
• 0
1
vote
8
replies
446
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
updated 23 hours ago by
Alex Reynolds
35k • written 5 days ago by
ntsopoul
▴ 60
1
vote
4
replies
311
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 16 hours ago by
Joe
21k • written 10 days ago by
cput
• 0
1
vote
16
replies
723
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
updated 13 hours ago by
GenoMax
142k • written 3 days ago by
hophuquy0944
• 0
1
vote
1
reply
143
views
constructing pangenome through psvcp
psvcp
pangenome
12 hours ago by
analyst
▴ 50
1
vote
1
reply
247
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 5 hours ago by
nguyenn6
• 0 • written 12 weeks ago by
star
▴ 10
1
vote
2
replies
595
views
Checking chromosome builds for genotyping data
GWAS
Liftover
PLINK
updated 10 minutes ago by
Muhammad
• 0 • written 2.6 years ago by
mari.johnson
• 0
0
votes
3
replies
364
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
5 days ago by
mropri
▴ 150
0
votes
1
reply
244
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA
RNA-seq
Nomalization
Microarray
updated 6 days ago by
Zhenyu Zhang
★ 1.2k • written 8 days ago by
jain72744
▴ 10
0
votes
0
replies
105
views
reference-free assembly error assessment tools
assembly
5 days ago by
lagartija
▴ 160
0
votes
2
replies
192
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
3 days ago by
melissa.joubert
• 0
0
votes
0
replies
86
views
News:
New course: Manipulation of NGS Data for Genomic and Population Genetics Analyses
KeepLearning
TScourses
3 days ago by
Transmitting Science communication
▴ 70
0
votes
0
replies
97
views
ReactomeGSA
ReactomeGSA
3 days ago by
Shaimaa Gamal
▴ 10
0
votes
1
reply
163
views
consensus sequence calling
consensus
updated 5 days ago by
bk11
★ 2.5k • written 5 days ago by
Ghada
• 0
0
votes
0
replies
105
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
5 days ago by
atariw
▴ 10
0
votes
1
reply
158
views
Mouse ribosome sequences in fasta format
fasta
mm10
rRNA
updated 5 days ago by
GenoMax
142k • written 6 days ago by
octpus616
▴ 100
0
votes
3
replies
167
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
3 days ago by
Esraa
• 0
0
votes
5
replies
323
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
5 days ago by
SilhouetteQ
• 0
0
votes
11
replies
550
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
6 days ago by
Tuck898
• 0
0
votes
9
replies
616
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
updated 3 days ago by
Wayne
★ 2.0k • written 12 days ago by
JACKY
▴ 140
0
votes
0
replies
111
views
genomic region of transcription factor
search
HOMER
motif
1 day ago by
qudrat.nii
▴ 10
0
votes
0
replies
110
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity
metatranscriptome
3 days ago by
jway
• 0
0
votes
1
reply
140
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
3 days ago by
asalimih
▴ 60
185 results • Page
2 of 4
Recent Votes
A: How is the design in DESeq2 work?
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
Answer: RNAseq coverage vs depth for transcript isoform expression?
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
Recent Locations •
All
Australia,
6 minutes ago
United States,
28 minutes ago
Hong Kong,
28 minutes ago
Australia,
30 minutes ago
Turkey,
38 minutes ago
USA,
42 minutes ago
United States,
46 minutes ago
Recent Awards •
All
Popular Question
to
Muhammad
• 0
Popular Question
to
synat.keam
▴ 100
Scholar
to
jv
★ 1.8k
Popular Question
to
syedahamdani94
• 0
Popular Question
to
mohammadhassanj
▴ 260
Scholar
to
dsull
★ 6.0k
Popular Question
to
finswimmer
16k
Recent Replies
Answer: Checking chromosome builds for genotyping data
by
Muhammad
• 0
Assume you have genotype data in Plink format. (G.bed, G.bim, G.fam) Download some reference panel data in Plink format (R.bed, R.bim, R.f…
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors)
by
nguyenn6
• 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed
by
anton.i.petrov
• 0
Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp
by
analyst
▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R
by
1769mkc
★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks
by
ATpoint
82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner
by
Joe
21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression?
by
Gordon Smyth
★ 7.2k
See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
Comment: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF)
by
aidangcruickshank
▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data?
by
Ngrin
• 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Traffic: 1034 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