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
182 results • Page
2 of 4
Sort: replies
Rank
Views
Votes
Replies
2
votes
4
replies
298
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
3 days ago by
Esraa
• 0
0
votes
4
replies
262
views
Galaxy StringTie error
stringtie
galaxy
4 days ago by
trkfs
• 0
6
votes
4
replies
304
views
Details on salmon index
Salmon
updated 1 day ago by
Rob
6.6k • written 2 days ago by
Lorenzo
• 0
4
votes
4
replies
3.0k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 4 days ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
1
vote
4
replies
285
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
2 days ago by
Arton
▴ 10
1
vote
4
replies
302
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 8 hours ago by
Joe
21k • written 9 days ago by
cput
• 0
1
vote
4
replies
290
views
Add stats to boxplot in R
stats
R
3 days ago by
Ghada
• 0
2
votes
4
replies
230
views
Help with IGV abbreviation
igv
updated 3 days ago by
Ram
43k • written 4 days ago by
GeneC
• 0
0
votes
4
replies
273
views
How to handle duplicated genes in TCGA data?
TCGA
GDC
mRNA
updated 11 hours ago by
txema.heredia
▴ 130 • written 1 day ago by
Ngrin
• 0
0
votes
4
replies
292
views
How to extract cells of different species after mapping with combined genome?
snRNA-seq
scRNA-seq
updated 1 day ago by
Tony
• 0 • written 2 days ago by
vk
▴ 10
2
votes
3
replies
215
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC
RNA-Seq
updated 3 days ago by
Ram
43k • written 4 days ago by
Prawesh
• 0
0
votes
3
replies
260
views
Sam file Header problem
Sam
Header
problem
file
updated 1 day ago by
Pierre Lindenbaum
161k • written 2 days ago by
saifulislam99121
• 0
1
vote
3
replies
437
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
0
votes
3
replies
358
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
3
replies
193
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat
single-cell
scRNA-seq
R
updated 4 days ago by
Ram
43k • written 5 days ago by
yau
• 0
3
votes
3
replies
271
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 4 days ago by
Ram
43k • written 18 days ago by
Adyasha
• 0
3
votes
3
replies
365
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 4 days ago by
Mathew
▴ 140 • written 7 days ago by
Christopher
• 0
0
votes
3
replies
349
views
Snakemake wrapper issue
fastqc
snakemake
updated 4 days ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
0
votes
3
replies
205
views
How to access GWAVA software of data
GWAVA
updated 4 days ago by
GenoMax
142k • written 4 days ago by
nonaddldy
▴ 10
0
votes
3
replies
215
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 4 days ago by
GenoMax
142k • written 4 days ago by
RNAseqer
▴ 270
2
votes
3
replies
278
views
Finding variants within a subset of a BAM file
variant
calling
4 days ago by
ramiro.barrantes
• 0
0
votes
3
replies
264
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 4 days ago by
noodle
▴ 580 • written 4 days ago by
doramora
▴ 10
0
votes
3
replies
165
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
3 days ago by
Esraa
• 0
1
vote
3
replies
285
views
Using ggplotly in R
ggplot
ggplotly
updated 3 days ago by
jared.andrews07
★ 16k • written 4 days ago by
jen
▴ 10
1
vote
3
replies
207
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
3
votes
3
replies
229
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
updated 2 days ago by
ATpoint
82k • written 3 days ago by
Alexandra
• 0
3
votes
3
replies
216
views
getting exon coordinates
genomics
updated 2 days ago by
Ram
43k • written 2 days ago by
Xbox_27
• 0
2
votes
3
replies
290
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio
Cibersort
R
5 days ago by
Azra
▴ 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 4 days ago by
ohtang7
▴ 40
1
vote
3
replies
800
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
3
replies
262
views
Tool:
Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes
Decimal
offtopic
Degrees
python
updated 1 day ago by
Ram
43k • written 3 days ago by
kuttibiotech2009
▴ 30
2
votes
3
replies
247
views
ggrepel function: geom_text_repel()
ggplot2
ggrepel
R
updated 1 day ago by
Ram
43k • written 2 days ago by
sooni
▴ 20
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 3 days ago by
mbrav005
• 0
2
votes
2
replies
185
views
Cannot install bwa-mem2 via conda
conda
mamba
python
updated 2 days ago by
Ram
43k • written 3 days ago by
jsmith120f
• 0
0
votes
2
replies
307
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 5 days ago by
Zhenyu Zhang
★ 1.2k • written 15 days ago by
yahn
• 0
0
votes
2
replies
189
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
2
replies
223
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
2 days ago by
Chen
• 0
0
votes
2
replies
435
views
News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
5 days ago by
David Langenberger
11k
1
vote
2
replies
228
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
2
replies
183
views
Duplicated sequence samtools
bowtie2
samtools
updated 5 days ago by
GenoMax
142k • written 5 days ago by
Moinuddin
• 0
0
votes
2
replies
210
views
Output file of samtools flagstat empty
samtools-flagstat
updated 5 days ago by
colindaven
6.4k • written 6 days ago by
ramendra.sarma
• 0
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
2
votes
2
replies
199
views
genome finishing
finishing
genome
updated 3 days ago by
nd48
▴ 20 • written 3 days ago by
trezini
• 0
3
votes
2
replies
195
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 5 days ago by
ATpoint
82k • written 5 days ago by
jennyp0706
• 0
2
votes
2
replies
226
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 2 days ago by
Ram
43k • written 2 days ago by
txema.heredia
▴ 130
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
0
votes
2
replies
198
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
melissachua90
▴ 70
2
votes
2
replies
206
views
Genome Visualization Tools
bacterial
genome
updated 4 days ago by
GenoMax
142k • written 4 days ago by
dlera.lozano
▴ 10
0
votes
2
replies
233
views
Obtaining Infinium Methylation450K manifest for hg38
TCGA
hg38
methylation
Illumina
updated 5 days ago by
Zhenyu Zhang
★ 1.2k • written 10 days ago by
elisheva
▴ 120
1
vote
2
replies
225
views
Doubt about the process of annotation, detection, identification and classification of transposable elements
annotation
TransposableElements
3 days ago by
MarcosCosta
• 0
182 results • Page
2 of 4
Recent Votes
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?
Answer: ChatGPT optimized for bioinformatics questions
Comment: ChatGPT optimized for bioinformatics questions
Recent Locations •
All
Finland,
2 minutes ago
United States,
2 minutes ago
UK,
7 minutes ago
Australia,
8 minutes ago
United States,
14 minutes ago
Germany,
14 minutes ago
United States,
18 minutes ago
Recent Awards •
All
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
Popular Question
to
Ezequiel
• 0
Popular Question
to
alanh
▴ 170
Recent Replies
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 precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167. Table 1 o…
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…
Comment: GG Sankey plot
by
LauferVA
4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Traffic: 1242 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