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Limit : this week
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184 results • Page
2 of 4
Sort: Votes
Rank
Views
Votes
Replies
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
5
replies
266
views
Annotating file using bcftools
annotation
plink
bcftools
2 days ago by
kl
▴ 10
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
2
replies
228
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
1
reply
142
views
constructing pangenome through psvcp
psvcp
pangenome
11 hours ago by
analyst
▴ 50
1
vote
1
reply
185
views
mitochondrial genome assembly pipeline
mammals
mitochondrial-genome
updated 2 days ago by
Ram
43k • written 2 days ago by
m90
▴ 30
1
vote
8
replies
443
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
updated 22 hours ago by
Alex Reynolds
35k • written 5 days ago by
ntsopoul
▴ 60
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
5
replies
318
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
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
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
2
replies
269
views
How to interpret infinite odds ratio?
statistics
4 days ago by
Lukas
• 0
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
2
replies
363
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 5 days ago by
Ram
43k • written 6 days ago by
t.fortunato.asquini
• 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
0
replies
130
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
5
replies
287
views
Can I perform a correlation test with 3 biological replicates per condition?
RNA-Seq
deseq2
updated 2 days ago by
Ram
43k • written 2 days ago by
manuelmourato25
• 0
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
1
reply
191
views
Tool:
Collect dispersed executable files and run them by using bingo.
bingo
updated 2 days ago by
Ram
43k • written 2 days ago by
dwpeng
▴ 10
1
vote
3
replies
271
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
243
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 4 hours ago by
nguyenn6
• 0 • written 12 weeks ago by
star
▴ 10
1
vote
4
replies
311
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 15 hours ago by
Joe
21k • written 10 days ago by
cput
• 0
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
1
reply
180
views
API kegg - IndexError: list index out of range
kegg
API
updated 1 day ago by
Nyksubuz
▴ 20 • written 2 days ago by
mirwa.zidi93
• 0
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
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
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
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
0
votes
4
replies
407
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
5 days ago by
beginner123
• 0
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
0
replies
69
views
Tera-scale metagenomic coassembly tool
co-assembly
Metagenomics
13 hours ago by
Moinuddin
• 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
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
0
votes
0
replies
113
views
DOCK6 installation on MacOS M1
installation
troubleshooting
DOCK6
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Rodolfo Adrián
• 0
0
votes
9
replies
604
views
Using VEP annotation output as the input for a second VEP annotation
Annotation
VEP
VCF
3 days ago by
Arton
▴ 10
0
votes
2
replies
226
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
3 days ago by
Chen
• 0
0
votes
5
replies
288
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 3 days ago by
GenoMax
142k • written 3 days ago by
chrisk
• 0
0
votes
4
replies
241
views
Sequencing Depth (Read Depth) Calculations
depth
3 days ago by
LucisTheFather
• 0
0
votes
0
replies
144
views
select set of intervals that cover a genomic region
GRanges
bed
2 days ago by
ntsopoul
▴ 60
0
votes
1
reply
590
views
scRNAseq quality control weird double curve in nFeature vs nCount plot
scRNA-seq
QC
single
cell
BDRhapsody
analysis
updated 2 days ago by
valdirbarth
▴ 20 • written 12 months ago by
Salomé
• 0
0
votes
9
replies
357
views
Duplicated reads (IDs) from nanopore sequencing
bam
nanopore
sequencing
2 days ago by
njornet
▴ 20
0
votes
0
replies
129
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
2 days ago by
ebertomeup
• 0
0
votes
0
replies
127
views
Blog:
The Current State and Future Prospects of Long-Read Sequencing
LRS
2 days ago by
Novogene
▴ 420
0
votes
2
replies
235
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
5 days ago by
analyst
▴ 50
184 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?
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Recent Replies
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.
Answer: Design for complex RNA-Seq experiment using Deseq2
by
swbarnes2
14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
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