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188 results • Page
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0
votes
4
replies
283
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
1 day ago by
mavy
▴ 10
0
votes
4
replies
322
views
Merge clusters in Seurat UMAP
seurat
umap
2 days ago by
kilcdincer
▴ 10
0
votes
4
replies
149
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
18 minutes ago by
Bibi
• 0
0
votes
4
replies
323
views
How to handle duplicated genes in TCGA data?
TCGA
GDC
mRNA
updated 1 day ago by
txema.heredia
▴ 130 • written 2 days ago by
Ngrin
• 0
0
votes
4
replies
326
views
How to extract cells of different species after mapping with combined genome?
snRNA-seq
scRNA-seq
updated 2 days ago by
Tony
• 0 • written 3 days ago by
vk
▴ 10
1
vote
4
replies
346
views
Contig assembly task, errors
dna
genetics
contig
assembly
updated 6 days ago by
Ram
43k • written 10 days ago by
samRayne
• 0
3
votes
4
replies
409
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
masspec
uORF
peptide
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Pierre Lindenbaum
161k
1
vote
4
replies
353
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 6 days ago by
Vijith
▴ 30
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 6 days ago by
Thind amarinder
▴ 340 • written 5.0 years ago by
garbuzov
▴ 70
3
votes
3
replies
247
views
getting exon coordinates
genomics
updated 3 days ago by
Ram
43k • written 3 days ago by
Xbox_27
• 0
2
votes
3
replies
291
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio
Cibersort
R
6 days ago by
Azra
▴ 10
1
vote
3
replies
447
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
6 days ago by
kalavattam
▴ 190
0
votes
3
replies
371
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
6 days ago by
mropri
▴ 150
0
votes
3
replies
198
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat
single-cell
scRNA-seq
R
updated 6 days ago by
Ram
43k • written 6 days ago by
yau
• 0
3
votes
3
replies
295
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 6 days ago by
Ram
43k • written 19 days ago by
Adyasha
• 0
3
votes
3
replies
368
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 5 days ago by
Mathew
▴ 140 • written 8 days ago by
Christopher
• 0
0
votes
3
replies
355
views
Snakemake wrapper issue
fastqc
snakemake
updated 5 days ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
0
votes
3
replies
211
views
How to access GWAVA software of data
GWAVA
updated 5 days ago by
GenoMax
142k • written 5 days ago by
nonaddldy
▴ 10
0
votes
3
replies
218
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 5 days ago by
GenoMax
142k • written 5 days ago by
RNAseqer
▴ 270
2
votes
3
replies
286
views
Finding variants within a subset of a BAM file
variant
calling
5 days ago by
ramiro.barrantes
• 0
0
votes
3
replies
268
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 5 days ago by
noodle
▴ 580 • written 5 days ago by
doramora
▴ 10
2
votes
3
replies
217
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC
RNA-Seq
updated 5 days ago by
Ram
43k • written 5 days ago by
Prawesh
• 0
0
votes
3
replies
170
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
4 days ago by
Esraa
• 0
1
vote
3
replies
294
views
Using ggplotly in R
ggplot
ggplotly
updated 4 days ago by
jared.andrews07
★ 16k • written 5 days ago by
jen
▴ 10
1
vote
3
replies
208
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
updated 4 days ago by
Zhenyu Zhang
★ 1.2k • written 4 days ago by
shpak.max
▴ 50
3
votes
3
replies
234
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
updated 3 days ago by
ATpoint
82k • written 4 days ago by
Alexandra
• 0
1
vote
3
replies
280
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 3 days ago by
GenoMax
142k • written 5 days ago by
ohtang7
▴ 40
1
vote
3
replies
803
views
About runing Pilon on individual chromosomes when polish draft genome assembly
Pilon
chromosome
polish
genome
draft
updated 3 days ago by
sansan_96
▴ 90 • written 2.7 years ago by
boymin2020
▴ 80
1
vote
3
replies
282
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 4 days ago by
kuttibiotech2009
▴ 30
2
votes
3
replies
253
views
ggrepel function: geom_text_repel()
ggplot2
ggrepel
R
updated 2 days ago by
Ram
43k • written 3 days ago by
sooni
▴ 20
0
votes
3
replies
280
views
Sam file Header problem
Sam
Header
problem
file
updated 2 days ago by
Pierre Lindenbaum
161k • written 3 days ago by
saifulislam99121
• 0
0
votes
2
replies
187
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
5 days ago by
IdaHao0921
• 0
0
votes
2
replies
200
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
6 hours ago by
Umer
▴ 50
0
votes
2
replies
245
views
Design for complex RNA-Seq experiment using Deseq2
Model.Matrix
RNA-Seq
Limma
DESeq2
edgeR
7 hours ago by
Ezequiel
• 0
0
votes
2
replies
302
views
Traveler with Infernal mapping failed
r2dt
updated 23 hours ago by
anton.i.petrov
• 0 • written 3 months ago by
Larissa
• 0
0
votes
2
replies
218
views
Output file of samtools flagstat empty
samtools-flagstat
updated 6 days ago by
colindaven
6.4k • written 7 days ago by
ramendra.sarma
• 0
2
votes
2
replies
261
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 3 days ago by
Ram
43k • written 3 days ago by
txema.heredia
▴ 130
1
vote
2
replies
234
views
Doubt about the process of annotation, detection, identification and classification of transposable elements
annotation
TransposableElements
4 days ago by
MarcosCosta
• 0
2
votes
2
replies
190
views
Cannot install bwa-mem2 via conda
conda
mamba
python
updated 3 days ago by
Ram
43k • written 4 days ago by
jsmith120f
• 0
0
votes
2
replies
214
views
Trimming tool
Trimmer
tool
updated 2 days ago by
ntsopoul
▴ 60 • written 2 days ago by
GeneC
• 0
1
vote
2
replies
251
views
is there a tool to recover corrupted fastq files
fastq
short-read
updated 1 hour ago by
Tommaso
• 0 • written 12 weeks ago by
pt.taklifi
▴ 60
0
votes
2
replies
312
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 6 days ago by
Zhenyu Zhang
★ 1.2k • written 16 days ago by
yahn
• 0
1
vote
2
replies
213
views
Alphafold 3 pLDDT coloring scheme in chimerax?
ChimeraX
Alphaphold
Alphaphold3
updated 4 days ago by
colindaven
6.4k • written 4 days ago by
mbrav005
• 0
3
votes
2
replies
288
views
imputation through beagle
panel
beagle
reference
imputation
5 days ago by
analyst
▴ 50
2
votes
2
replies
208
views
Genome Visualization Tools
bacterial
genome
updated 5 days ago by
GenoMax
142k • written 5 days ago by
dlera.lozano
▴ 10
0
votes
2
replies
194
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
4 days ago by
melissa.joubert
• 0
1
vote
2
replies
671
views
Checking chromosome builds for genotyping data
GWAS
Liftover
PLINK
updated 18 hours ago by
Muhammad
• 0 • written 2.6 years ago by
mari.johnson
• 0
0
votes
2
replies
236
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
6 days ago by
analyst
▴ 50
2
votes
2
replies
203
views
genome finishing
finishing
genome
updated 4 days ago by
nd48
▴ 20 • written 4 days ago by
trezini
• 0
0
votes
2
replies
234
views
Obtaining Infinium Methylation450K manifest for hg38
TCGA
hg38
methylation
Illumina
updated 6 days ago by
Zhenyu Zhang
★ 1.2k • written 11 days ago by
elisheva
▴ 120
188 results • Page
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Recent Votes
Comment: Add stats to the plot
Post-doctoral Position in Alzheimer’s Disease Genetics, ‘Omics, and Biomarkers
The Biostar Handbook. A bioinformatics e-book for beginners.
Answer: How to add Ensembl id to cluster.markers in Seurat
How to add Ensembl id to cluster.markers in Seurat
Comment: Duplicated sequence samtools
Answer: Duplicated sequence samtools
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Recent Replies
Answer: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
Bibi
• 0
@atpoint thanks you for your timely response. Can someone else shed light if we can compare the trend of DEGs using the scRNA and Bulk RNA…
Comment: Add stats to the plot
by
GenoMax
142k
Please use `101010` to format `code` so it is represented in monospace font. I have done this for you now.
Answer: is there a tool to recover corrupted fastq files
by
Tommaso
• 0
You may also want to give a try to **FastqWiper** (https://github.com/mazzalab/fastqwiper)
Comment: Add stats to the plot
by
Ghada
• 0
Thanks. That helpful. I am getting this error data4_test <- data4.ts%>% ungroup() %>% t.test(data =.,value ~ Condition)%>% + …
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
ATpoint
82k
I cannot comment here. You are asking why results between two experiments are different. I do not know without seeing the data.
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
Bibi
• 0
Thank you so much for this insight. I just want to clarify another point here. I have used scRNA seq data from mice mammary epithelial cell…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
Pierre Lindenbaum
161k
> Cannot read non-existent file: file:///local/home/User/VCF_Filtering/biostar.code your file doesn't exist, is at the wrong place etc.
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
ajbarrett98
• 0
Hi Pierre, I am attempting to run this code and am running into this error: (jvar) $ jvarkit vcffilterjdk -f biostar.code Dart_VCF2_Or…
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
ATpoint
82k
I cannot give a precise answer, as ML is not my field, but generally, why don't you apply the method to pseudobulks of the exact single-cel…
Answer: geom_bar issue in ggplot2 with xlim()
by
ATpoint
82k
https://stackoverflow.com/questions/10365167/geom-bar-bars-not-displaying-when-specifying-ylim
Comment: What marks a De-Novo Genome assembly as FAILED?
by
Umer
▴ 50
Yes. We are sequencing 45 different samples with illumina. 12 of these are also going to be sequenced with Nanopore (for hybrid assembly). …
Comment: HGVS Nomenclature of Multiple Indels found in Cis
by
LauferVA
4.2k
how has this code progressed? is it publically available? would you want to work together?
Comment: Design for complex RNA-Seq experiment using Deseq2
by
Ezequiel
• 0
I completely agree with most points. The PCA shows that the biggest driver of difference is the patients themselves, with PRE and POST time…
Comment: Add stats to the plot
by
marco.barr
▴ 130
Hi, you can add statistical annotations using `ggpubr` function `stat_pvalue_manual `. You need to make sure you calculate the p-values fir…
Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
by
ATpoint
82k
Use everything before the whitespace in list.txt, for example `A00869:294:HCW57DSXY:2:1101:3929:1000` and not `A00869:294:HCW57DSXY:2:1101:…
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