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189 results • Page
2 of 4
Sort: Views
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Views
Votes
Replies
3
votes
1
reply
330
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
updated 4 days ago by
dariober
14k • written 6 days ago by
Holly
▴ 30
0
votes
5
replies
330
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
6 days ago by
SilhouetteQ
• 0
1
vote
4
replies
330
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 1 day ago by
Joe
21k • written 11 days ago by
cput
• 0
0
votes
4
replies
330
views
Merge clusters in Seurat UMAP
seurat
umap
2 days ago by
kilcdincer
▴ 10
0
votes
4
replies
328
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 4 days ago by
vk
▴ 10
1
vote
5
replies
316
views
Can I perform a correlation test with 3 biological replicates per condition?
RNA-Seq
deseq2
updated 3 days ago by
Ram
43k • written 3 days ago by
manuelmourato25
• 0
2
votes
4
replies
310
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
4 days ago by
Esraa
• 0
0
votes
5
replies
306
views
calculating genomic coverage/ base overlap in R
genomics
updated 1 day ago by
1769mkc
★ 1.2k • written 4 days ago by
Xbox_27
• 0
0
votes
2
replies
302
views
Traveler with Infernal mapping failed
r2dt
updated 1 day ago by
anton.i.petrov
• 0 • written 3 months ago by
Larissa
• 0
1
vote
4
replies
298
views
Add stats to boxplot in R
stats
R
4 days ago by
Ghada
• 0
1
vote
1
reply
297
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 1 day ago by
nguyenn6
• 0 • written 3 months ago by
star
▴ 10
1
vote
4
replies
297
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
4 days ago by
Arton
▴ 10
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
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
2
replies
292
views
is there a tool to recover corrupted fastq files
fastq
short-read
updated 8 hours ago by
Tommaso
• 0 • written 12 weeks ago by
pt.taklifi
▴ 60
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
0
votes
5
replies
290
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 4 days ago by
GenoMax
142k • written 4 days ago by
chrisk
• 0
2
votes
3
replies
289
views
Finding variants within a subset of a BAM file
variant
calling
5 days ago by
ramiro.barrantes
• 0
3
votes
2
replies
289
views
imputation through beagle
panel
beagle
reference
imputation
5 days ago by
analyst
▴ 50
2
votes
5
replies
288
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 6 days ago by
Philipp Bayer
8.5k • written 6 days ago by
林明德
• 0
1
vote
3
replies
285
views
Tool:
Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes
Decimal
offtopic
Degrees
python
updated 3 days ago by
Ram
43k • written 4 days ago by
kuttibiotech2009
▴ 30
0
votes
4
replies
284
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
1 day ago by
mavy
▴ 10
1
vote
3
replies
282
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 3 days ago by
GenoMax
142k • written 6 days ago by
ohtang7
▴ 40
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
2
votes
4
replies
275
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 4 days ago by
yura.grabovska
▴ 90 • written 4 days ago by
ev97
▴ 20
2
votes
2
replies
270
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
5
replies
269
views
Annotating file using bcftools
annotation
plink
bcftools
3 days ago by
kl
▴ 10
1
vote
2
replies
269
views
How to interpret infinite odds ratio?
statistics
5 days ago by
Lukas
• 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
0
votes
4
replies
268
views
Galaxy StringTie error
stringtie
galaxy
5 days ago by
trkfs
• 0
0
votes
2
replies
263
views
Design for complex RNA-Seq experiment using Deseq2
Model.Matrix
RNA-Seq
Limma
DESeq2
edgeR
14 hours ago by
Ezequiel
• 0
2
votes
3
replies
253
views
ggrepel function: geom_text_repel()
ggplot2
ggrepel
R
updated 3 days ago by
Ram
43k • written 4 days ago by
sooni
▴ 20
3
votes
3
replies
250
views
getting exon coordinates
genomics
updated 3 days ago by
Ram
43k • written 3 days ago by
Xbox_27
• 0
1
vote
1
reply
249
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
4 days ago by
ramiro.barrantes
• 0
0
votes
1
reply
248
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Mendelian-Randomization
updated 6 days ago by
Ram
43k • written 10 days ago by
Nikki
• 0
0
votes
4
replies
246
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
7 hours ago by
Bibi
• 0
0
votes
4
replies
246
views
Sequencing Depth (Read Depth) Calculations
depth
4 days ago by
LucisTheFather
• 0
2
votes
4
replies
236
views
Help with IGV abbreviation
igv
updated 5 days ago by
Ram
43k • written 6 days ago by
GeneC
• 0
0
votes
2
replies
237
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 2 days ago by
Pierre Lindenbaum
161k • written 3 days ago by
melissachua90
▴ 70
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
1
vote
2
replies
235
views
Doubt about the process of annotation, detection, identification and classification of transposable elements
annotation
TransposableElements
4 days ago by
MarcosCosta
• 0
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
2
replies
233
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
0
votes
2
replies
231
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
4 days ago by
Chen
• 0
0
votes
2
replies
229
views
GG Sankey plot
GO
sankey_plot
gglpot
updated 2 days ago by
LauferVA
4.2k • written 2 days ago by
ijarne
• 0
1
vote
5
replies
227
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
0
votes
2
replies
225
views
Trimming tool
Trimmer
tool
updated 2 days ago by
ntsopoul
▴ 60 • written 2 days ago by
GeneC
• 0
0
votes
3
replies
220
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 5 days ago by
GenoMax
142k • written 6 days ago by
RNAseqer
▴ 270
3
votes
1
reply
220
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
updated 6 days ago by
aw7
▴ 300 • written 11 days ago by
Zeng Hao
▴ 40
0
votes
2
replies
219
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
189 results • Page
2 of 4
Recent Votes
A: How To Split One Big Sequence File Into Multiple Files With Less Than 1000 Seque
C: Snakemake vs. Nextflow: strengths and weaknesses
Answer: workflow management system : WDL, CWL, Ruffus, SnakeMake, etc
Sequence alignment on split read event such as inversion, duplication and complex nested events.
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
Comment: Add stats to the plot
Post-doctoral Position in Alzheimer’s Disease Genetics, ‘Omics, and Biomarkers
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Recent Awards •
All
Scholar
to
Pierre Lindenbaum
161k
Voter
to
Sara
▴ 30
Popular Question
to
carlopecoraro2
★ 2.5k
Popular Question
to
scideas
▴ 30
Popular Question
to
Muhammad
• 0
Popular Question
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synat.keam
▴ 100
Scholar
to
jv
★ 1.8k
Recent Replies
Comment: BiomartException: Query ERROR for existing dataset in BioMart
by
Luqman
• 0
I am using *pybiomart* which has Server inplace of BiomartServer, I used that as per above but still getting the same error. Also, when I a…
Comment: Blastn, need help to increase speed
by
m13113153781
• 0
mmseq2 is indeed a good acceleration solution, but its index files require ~ 6 T space....
Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
by
KHURRAM SHAHZAD
• 0
Thank you it works
Answer: Add stats to the plot
by
Ghada
• 0
I think this is what caused the error. we do not have group 1 and 2 in the statistical test results???? ![enter image description here][…
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). …
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