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181 results • Page
2 of 4
Sort: replies
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Views
Votes
Replies
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
3
votes
4
replies
370
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
masspec
uORF
peptide
updated 2 days ago by
GenoMax
142k • written 2 days ago by
Pierre Lindenbaum
161k
1
vote
4
replies
289
views
Add stats to boxplot in R
stats
R
2 days ago by
Ghada
• 0
0
votes
4
replies
260
views
How to handle duplicated genes in TCGA data?
TCGA
GDC
mRNA
updated 5 hours ago by
txema.heredia
▴ 130 • written 1 day ago by
Ngrin
• 0
0
votes
4
replies
262
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
5 hours ago by
mavy
▴ 10
2
votes
4
replies
5.6k
views
44% Successfully Assigned Fragments with featureCounts after 85% uniquely mapped reads with STAR
rna-seq
alignment
RNA-Seq
featureCounts
STAR
updated 5 days ago by
Thind amarinder
▴ 340 • written 5.0 years ago by
garbuzov
▴ 70
6
votes
4
replies
297
views
Details on salmon index
Salmon
updated 1 day ago by
Rob
6.6k • written 2 days ago by
Lorenzo
• 0
3
votes
4
replies
288
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
patch
freeze
genome
updated 23 hours ago by
Jeremy Leipzig
22k • written 2 days ago by
Ali
• 0
0
votes
4
replies
279
views
Merge clusters in Seurat UMAP
seurat
umap
1 day ago by
kilcdincer
▴ 10
1
vote
4
replies
287
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 2 hours ago by
Joe
21k • written 9 days ago by
cput
• 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
4 days ago by
kalavattam
▴ 190
0
votes
3
replies
254
views
Sam file Header problem
Sam
Header
problem
file
updated 1 day ago by
Pierre Lindenbaum
161k • written 2 days ago by
saifulislam99121
• 0
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
0
votes
3
replies
192
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
2
votes
3
replies
289
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
0
votes
3
replies
264
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 3 days ago by
noodle
▴ 580 • written 3 days ago by
doramora
▴ 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 3 days ago by
Prawesh
• 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
2
votes
3
replies
241
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
3
replies
255
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
1
vote
3
replies
206
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
updated 2 days ago by
Zhenyu Zhang
★ 1.2k • written 2 days ago by
shpak.max
▴ 50
0
votes
3
replies
204
views
How to access GWAVA software of data
GWAVA
updated 4 days ago by
GenoMax
142k • written 4 days ago by
nonaddldy
▴ 10
1
vote
3
replies
797
views
About runing Pilon on individual chromosomes when polish draft genome assembly
Pilon
chromosome
polish
genome
draft
updated 1 day ago by
sansan_96
▴ 90 • written 2.7 years ago by
boymin2020
▴ 80
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
212
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 4 days ago by
GenoMax
142k • written 4 days ago by
RNAseqer
▴ 270
1
vote
3
replies
283
views
Using ggplotly in R
ggplot
ggplotly
updated 2 days ago by
jared.andrews07
★ 16k • written 3 days ago by
jen
▴ 10
1
vote
3
replies
272
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 1 day ago by
GenoMax
142k • written 4 days ago by
ohtang7
▴ 40
0
votes
3
replies
356
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
4 days ago by
mropri
▴ 150
0
votes
3
replies
347
views
Snakemake wrapper issue
fastqc
snakemake
updated 4 days ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
3
votes
3
replies
208
views
getting exon coordinates
genomics
updated 1 day ago by
Ram
43k • written 2 days ago by
Xbox_27
• 0
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
2
votes
3
replies
277
views
Finding variants within a subset of a BAM file
variant
calling
3 days ago by
ramiro.barrantes
• 0
2
votes
2
replies
219
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 1 day ago by
Ram
43k • written 1 day ago by
txema.heredia
▴ 130
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 9 days ago by
elisheva
▴ 120
0
votes
2
replies
305
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 5 days ago by
Zhenyu Zhang
★ 1.2k • written 14 days ago by
yahn
• 0
0
votes
2
replies
232
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
5 days ago by
analyst
▴ 50
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
3
votes
2
replies
194
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
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 4 days ago by
Ram
43k • written 5 days ago by
t.fortunato.asquini
• 0
1
vote
2
replies
181
views
Duplicated sequence samtools
bowtie2
samtools
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Moinuddin
• 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
4 days ago by
David Langenberger
11k
1
vote
2
replies
1.3k
views
Extracting named fasta sequences according to list with Biopython
Biopython
FASTA
updated 4 days ago by
Rubayetul
• 0 • written 2.6 years ago by
lachiemck
• 0
3
votes
2
replies
286
views
imputation through beagle
panel
beagle
reference
imputation
4 days ago by
analyst
▴ 50
0
votes
2
replies
181
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
4 days ago by
IdaHao0921
• 0
1
vote
2
replies
269
views
How to interpret infinite odds ratio?
statistics
4 days ago by
Lukas
• 0
2
votes
2
replies
205
views
Genome Visualization Tools
bacterial
genome
updated 3 days ago by
GenoMax
142k • written 3 days ago by
dlera.lozano
▴ 10
1
vote
2
replies
210
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
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
2
votes
2
replies
197
views
genome finishing
finishing
genome
updated 2 days ago by
nd48
▴ 20 • written 3 days ago by
trezini
• 0
1
vote
2
replies
222
views
Doubt about the process of annotation, detection, identification and classification of transposable elements
annotation
TransposableElements
2 days ago by
MarcosCosta
• 0
181 results • Page
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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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Comment: ChatGPT optimized for bioinformatics questions
C: How can I perform Differential expression analysis with just one control and one
C: How can I perform Differential expression analysis with just one control and one
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Recent Replies
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
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hophuquy0944
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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
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Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF)
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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.
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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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@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
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Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
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You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
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ntsopoul
▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
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