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188 results • Page
2 of 4
Sort: Votes
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Votes
Replies
1
vote
2
replies
269
views
How to interpret infinite odds ratio?
statistics
5 days ago by
Lukas
• 0
1
vote
1
reply
149
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 5 days ago by
Ram
43k • written 5 days ago by
kilcdincer
▴ 10
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
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
1
vote
5
replies
226
views
Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
circos
atacseq
updated 4 days ago by
Pierre Lindenbaum
161k • written 4 days ago by
biology_inform
▴ 50
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
5
replies
802
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 4 days ago by
Zhenyu Zhang
★ 1.2k • written 4 days ago by
shpak.max
▴ 50
1
vote
4
replies
297
views
Add stats to boxplot in R
stats
R
4 days ago by
Ghada
• 0
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
1
vote
1
reply
249
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
4 days ago by
ramiro.barrantes
• 0
1
vote
4
replies
296
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
4 days ago by
Arton
▴ 10
1
vote
5
replies
269
views
Annotating file using bcftools
annotation
plink
bcftools
3 days ago by
kl
▴ 10
1
vote
1
reply
209
views
mitochondrial genome assembly pipeline
mammals
mitochondrial-genome
updated 3 days ago by
Ram
43k • written 3 days ago by
m90
▴ 30
1
vote
2
replies
232
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
3 days ago by
bioinfo
▴ 150
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
1
reply
192
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 3 days ago by
Jordan M Eizenga
▴ 460 • written 13 days ago by
sarumonsus
▴ 10
1
vote
0
replies
155
views
News:
Course on Manual Genome Curation
Genome-Assembly
Pretext-View
Manual-Genome-Curation
updated 2 days ago by
Ram
43k • written 3 days ago by
carlopecoraro2
★ 2.5k
1
vote
5
replies
315
views
Can I perform a correlation test with 3 biological replicates per condition?
RNA-Seq
deseq2
updated 2 days ago by
Ram
43k • written 3 days ago by
manuelmourato25
• 0
1
vote
1
reply
195
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
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
1
vote
1
reply
199
views
API kegg - IndexError: list index out of range
kegg
API
updated 2 days ago by
Nyksubuz
▴ 20 • written 3 days ago by
mirwa.zidi93
• 0
1
vote
5
replies
342
views
Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 2 days ago by
dthorbur
★ 2.0k • written 2 days ago by
BATMAN
• 0
1
vote
8
replies
460
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
updated 1 day ago by
Alex Reynolds
35k • written 5 days ago by
ntsopoul
▴ 60
1
vote
4
replies
323
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 1 day ago by
Joe
21k • written 10 days ago by
cput
• 0
1
vote
16
replies
745
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
updated 1 day ago by
GenoMax
142k • written 4 days ago by
hophuquy0944
• 0
1
vote
1
reply
175
views
constructing pangenome through psvcp
psvcp
pangenome
1 day ago by
analyst
▴ 50
1
vote
1
reply
288
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 22 hours ago by
nguyenn6
• 0 • written 12 weeks ago by
star
▴ 10
1
vote
2
replies
671
views
Checking chromosome builds for genotyping data
GWAS
Liftover
PLINK
updated 17 hours ago by
Muhammad
• 0 • written 2.6 years ago by
mari.johnson
• 0
1
vote
6
replies
1.4k
views
CellRanger output more cells than specified using --force-cells? Why?
scRNA-seq
cellranger
updated 15 hours ago by
scideas
▴ 30 • written 8 months ago by
rohitsatyam102
▴ 870
1
vote
0
replies
77
views
Tool:
Sequence alignment on split read event such as inversion, duplication and complex nested events.
minimap
alignment
NGMLR
12 hours ago by
micah
▴ 10
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
1
vote
3
replies
132
views
Add stats to the plot
R
stats
plotting
updated 1 hour ago by
GenoMax
142k • written 11 hours ago by
Ghada
• 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
0
votes
1
reply
165
views
consensus sequence calling
consensus
updated 6 days ago by
bk11
★ 2.5k • written 6 days ago by
Ghada
• 0
0
votes
0
replies
106
views
How can i use ESM-1v ?
VEP
ESM-1v
1 day ago by
Meto
• 0
0
votes
9
replies
650
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
updated 4 days ago by
Wayne
★ 2.0k • written 13 days ago by
JACKY
▴ 140
0
votes
7
replies
4.3k
views
B allele frequency (BAF)
snp
updated 1 day ago by
aidangcruickshank
▴ 10 • written 3.7 years ago by
rthapa
▴ 90
0
votes
0
replies
110
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity
metatranscriptome
4 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
4 days ago by
asalimih
▴ 60
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 9 days ago by
jain72744
▴ 10
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
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
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
0
replies
114
views
DOCK6 installation on MacOS M1
installation
troubleshooting
DOCK6
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Rodolfo Adrián
• 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
0
votes
1
reply
138
views
Broad and Narrow peaks
ATAC
ChIP
seq
updated 1 day ago by
ATpoint
82k • written 1 day ago by
Jacek
▴ 20
0
votes
0
replies
105
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
6 days ago by
atariw
▴ 10
0
votes
9
replies
606
views
Using VEP annotation output as the input for a second VEP annotation
Annotation
VEP
VCF
4 days ago by
Arton
▴ 10
188 results • Page
2 of 4
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 Awards •
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Pierre Lindenbaum
161k
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▴ 30
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★ 2.5k
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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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