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330 results • Page
1 of 7
Sort: Votes
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Views
Votes
Replies
9
votes
15
replies
847
views
Construction of single sequence assembly out of contigs
Contigs
Bacteria
Genome
WGS
8 days ago by
analyst
▴ 10
6
votes
3
replies
265
views
How can I adjust Y-axis scale when making relative abundance box plot ?
statistics
box-plot
R
scale_adjustment
logarithm
updated 7 days ago by
Jeremy
▴ 860 • written 7 days ago by
ohtang7
▴ 40
5
votes
3
replies
344
views
Strand bias in supplementary alignments from Nanopore
minimap2
nanopore
strand
updated 29 days ago by
cmdcolin
★ 3.4k • written 29 days ago by
dariober
14k
5
votes
2
replies
256
views
RNA Contamination Tool for Developing Cell Samples
contamination
scRNA
quality
RNA
SoupX
12 days ago by
Rafael Soler
★ 1.2k
4
votes
6
replies
441
views
bwa mem hangs after a few thousand reads
bwa-mem
alignment
bwa
calling
variant
7 days ago by
cee28
▴ 30
4
votes
2
replies
272
views
KEGG DATABASE
DATABASE
KEGG
updated 1 day ago by
jv
★ 1.3k • written 4 days ago by
Sijjil
• 0
4
votes
7
replies
565
views
SNP IDs
SNP
21 days ago by
kl
▴ 10
4
votes
6
replies
408
views
Unexpected separation of RNA-seq samples on PCA plot
depletion
PCA
rRNA
plot
RNA-seq
16 days ago by
Tihana
▴ 10
4
votes
9
replies
719
views
Snakemake issue with wrappers
Python
Snakemake
29 days ago by
Begonia_pavonina
▴ 120
3
votes
4
replies
433
views
Downstream analysis with DEseq2 normalization
DEseq2
integration
16 days ago by
QX
• 0
3
votes
7
replies
586
views
IGV not showing bigwig track information
bigwig
IGV
ChIP-seq
updated 22 days ago by
ATpoint
78k • written 26 days ago by
Rory Osborne
▴ 10
3
votes
2
replies
252
views
t-test by row
R
t-test
updated 14 days ago by
dthorbur
▴ 890 • written 15 days ago by
sooni
▴ 10
3
votes
6
replies
468
views
scRNA-seq: Consistent low number of cells and low fraction reads across the samples
scRNA-seq
cells
mRNA
expression
gene
updated 5 days ago by
jv
★ 1.3k • written 7 days ago by
newbee
▴ 40
3
votes
1
reply
149
views
GEO dataset Microarray data analysis help
R
microarray
NCBI
GEO
updated 1 day ago by
Ram
41k • written 2 days ago by
Confused_human
▴ 20
3
votes
4
replies
336
views
Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not present in R
FDR
volcano
plotting
R
plot
updated 7 days ago by
Nitin Narwade
★ 1.5k • written 8 days ago by
RNAseqer
▴ 250
3
votes
3
replies
304
views
How to proceed after Kraken2 analysis
rnaseq
kraken
updated 28 days ago by
dthorbur
▴ 890 • written 28 days ago by
pixie@bioinfo
★ 1.5k
2
votes
2
replies
829
views
Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when pivoting from wide to long format
rnaseq
pivot_longer
ggplot2
updated 8 days ago by
cmdcolin
★ 3.4k • written 8 days ago by
Dylan C-C
• 0
2
votes
2
replies
216
views
R script in docker
R
Visual_studio_code
Docker
6 days ago by
mrashad
▴ 70
2
votes
2
replies
292
views
Wrong in Deeptools : the enrichment of TSS and TES region are similar when using scale-region
plotprofile
computematrix
Deeptools
scale-region
13 days ago by
hao
▴ 10
2
votes
5
replies
368
views
kraken2 bacteria database 250GB+
metagenomics
16s
kraken2
kraken
updated 28 days ago by
GenoMax
136k • written 28 days ago by
10mz1
• 0
2
votes
2
replies
598
views
6 follow
Why runing scDblFinder before and after removing low QC cells gives different results
singleCellExperiment
scDblFinder
SMART-Seq
updated 9 days ago by
e.r.zakiev
▴ 170 • written 5 months ago by
Assa Yeroslaviz
★ 1.8k
2
votes
4
replies
299
views
An issue with gtf file (ballgownrsem)
Ballgown
RNA-seq
GTF
RSEM
17 hours ago by
cucindarko51
• 0
2
votes
2
replies
242
views
Compare similarity of protein variants
protein
structure
updated 20 days ago by
dthorbur
▴ 890 • written 21 days ago by
GP
• 0
2
votes
2
replies
210
views
4 Fastq files for a single run generated by 10X
scRNA-Seq
Fastq
SRA
10X
1 day ago by
hkarakurt
▴ 180
2
votes
3
replies
452
views
How to check if my sequence is DNA or Protein in BioPython?
genomics
biopython
fasta
updated 23 days ago by
Joe
21k • written 26 days ago by
O.rka
▴ 710
2
votes
2
replies
310
views
DESeq2 installation failures
DEseq2
updated 17 days ago by
Michael
53k • written 19 days ago by
dantuluri
• 0
2
votes
6
replies
2.1k
views
No best K value found
Assembly
Kmergenie
updated 12 days ago by
shaileshdesai76
• 0 • written 6.8 years ago by
kspata
▴ 80
2
votes
11
replies
694
views
Data preparation for a ML model
machine-learning
RNA-Seq
R
python
biomarkers
6 days ago by
sil_bioinfo
▴ 40
2
votes
1
reply
164
views
Extract variants from 100 000 genomes project
variants
100000-genomes-project
updated 16 days ago by
Ram
41k • written 16 days ago by
Mairena
• 0
2
votes
5
replies
231
views
kallisto index build difference according to version
index
version
kallisto
updated 2 days ago by
dsull
★ 5.1k • written 2 days ago by
estilo
• 0
2
votes
5
replies
711
views
Pre-processing for Agilent microarray data?
affymetrix
microarray
gene
agilent
rna
updated 20 days ago by
1769mkc
★ 1.1k • written 6 months ago by
survive
• 0
2
votes
1
reply
252
views
EnhancedVolcano underrepresenting DEGs
R
updated 8 days ago by
Kevin Blighe
86k • written 10 days ago by
jabbari.parnian
▴ 30
2
votes
4
replies
262
views
error when installing gistic2 using conda
conda
gistic2
updated 1 day ago by
Ram
41k • written 2 days ago by
luckyday1661
• 0
2
votes
6
replies
510
views
Annotating genome based on Sequence
genome
annotation
updated 28 days ago by
Darked89
4.5k • written 5 weeks ago by
buhbs
▴ 10
2
votes
3
replies
323
views
Selecting a subset of MSigDB database for GSEA
fgsea
clusterprofiler
GSEA
20 days ago by
Orange
▴ 10
2
votes
1
reply
169
views
unicycler error : [Errno 13] Permission denied:
unicycler
updated 8 days ago by
barslmn
★ 2.0k • written 8 days ago by
jiyoung
▴ 20
2
votes
6
replies
474
views
Burrows-Wheeler transform
Python
BWT
DNA
updated 23 days ago by
Ram
41k • written 24 days ago by
Balqees
• 0
2
votes
4
replies
406
views
What are the steps for Germline and Somatic CNV detection using CNVkit?
cnv
cnvkit
18 days ago by
ahmad mousavi
▴ 770
2
votes
3
replies
150
views
Annotation Visualization IGV
igv
alignment
gff
annotation
visualization
updated 11 hours ago by
Pierre Lindenbaum
158k • written 12 hours ago by
awhale01
• 0
2
votes
9
replies
696
views
Salmon (or other pseudo-mappers) for multi-species RNAseq read filtering
STAR
Salmon
mapper
aligner
RNAseq
7 days ago by
ian.will
▴ 10
1
vote
3
replies
283
views
Should unique gene names/transcript IDs be used for ribosomal gene copies in a GTF/GFF file?
GTF
GFF
updated 20 days ago by
dthorbur
▴ 890 • written 22 days ago by
cyril-cros
▴ 940
1
vote
3
replies
283
views
PMID multiple pdfs download using R
R
PubMed
updated 22 days ago by
Ram
41k • written 23 days ago by
Confused_human
▴ 20
1
vote
8
replies
532
views
DESEQ2 design in DESeqDataSetFromMatrix: cell and treatment
rna-seq
deseq2
17 days ago by
pingu77
▴ 20
1
vote
6
replies
528
views
frequency plot for peaks
chip-seq
chipseeker
updated 8 days ago by
Ankit
▴ 400 • written 23 days ago by
Mehwish
▴ 10
1
vote
3
replies
2.2k
views
BBMap : NH:i:1 and XT:A:R
bbmap
updated 14 days ago by
ayaosama2111
▴ 10 • written 7.1 years ago by
Nicolas Rosewick
10k
1
vote
4
replies
423
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
20 days ago by
Daniel
▴ 30
1
vote
9
replies
621
views
Command line or python RNA-seq read simulator
simulation
RNA-seq
26 days ago by
i.sudbery
18k
1
vote
1
reply
206
views
How to properly quantify gene expression of tandem duplicates from RNA-seq
pipeline
illumina
plants
RNA-seq
updated 23 days ago by
dthorbur
▴ 890 • written 24 days ago by
missTique
• 0
1
vote
4
replies
290
views
Bowtie mapping for single_end read
bowtie
8 days ago by
Rita
• 0
1
vote
2
replies
307
views
featureCounts error???
featureCounts
error
updated 24 days ago by
Gordon Smyth
★ 6.5k • written 25 days ago by
Samer
• 0
330 results • Page
1 of 7
Recent Votes
C: PCA vs ICA prior to t-SNE or UMAP
C: PCA vs ICA prior to t-SNE or UMAP
Answer: Calculate GC content for entire chromosome
Comment: Annotation Visualization IGV
Comment: Annotation Visualization IGV
Answer: Execute R command on specific termimal
Answer: Where can I get a list of SNPs mapping overlapping genes in humans?
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3.5k
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Recent Replies
Answer: RNA-Seq Data Analysis Workshop (March 11 - 14, 2024 in Berlin, Germany)
by
David Langenberger
10k
We already have an incredible number of registrations for this time. If you still want to be there, then you should register soon!
Comment: scRNA data analysis , how to compare pattern in multiple samples
by
ATpoint
78k
Can you please ask a precise question rather than posting a wall of code? What is the main problem you have, what did you try? Did you foll…
Comment: vcftools
by
sevda
• 0
Hello, Thank you for your attention. It ran successfully and I got no errors or warnings but no new files were created.
Comment: Resolving over clustered NGS with Q-scores
by
sam.himes92
• 0
The system that we used was [Aviti][1]. Our sequencing core was the one who quantified the loading/library concentration. Sorry I don't hav…
Comment: Where can I get a list of SNPs mapping overlapping genes in humans?
by
Alex Reynolds
35k
I modified the answer with an approach for that use case.
Comment: Where can I get a list of SNPs mapping overlapping genes in humans?
by
Ram
41k
OP is looking for overlapping genes - genes with presumably different gene IDs that share some loci. I think the `genes.bed` creation logic…
Comment: Where can I get a list of SNPs mapping overlapping genes in humans?
by
Alex Reynolds
35k
Note: The file `snps.bed` will be very large. You'll need sufficient disk space for this step.
Answer: Where can I get a list of SNPs mapping overlapping genes in humans?
by
Alex Reynolds
35k
Given files `genes.bed` and `snps.bed`, you could do something like: ``` $ bedmap --echo --echo-map-id --delim '\t' genes.bed snps.bed > a…
Answer: How to add exon annotations to genome annotation
by
alex.zaccaron
▴ 380
You can use [AGAT][1] to process your annotation file to add the missing exons. I believe `agat_convert_sp_gxf2gxf.pl -g no_exons.gff -o wi…
Comment: Annotation Visualization IGV
by
Pierre Lindenbaum
158k
and you got answer that should be validate (green tick), or people asked you questions but got no answers.
Comment: Annotation Visualization IGV
by
awhale01
• 0
Correct I have asked those questions before.
Comment: Annotation Visualization IGV
by
Pierre Lindenbaum
158k
you asked questions before: review, comment and/or validate them please: https://www.biostars.org/p/9530777/ ; https://www.biostars.org/p/9…
Comment: Ambient RNA removal method that generates whole (integer) counts
by
EK
• 0
Thanks, Jared. Sounds like rounding counts is the simplest approach for now. :)
Comment: Resolving over clustered NGS with Q-scores
by
Trivas
★ 1.5k
Could you tell us which sequencer you used, how you quantified your library size and concentration, and what your loading concentration was…
Comment: Resolving over clustered NGS with Q-scores
by
sam.himes92
• 0
I should have mentioned, we ran both Read 1 and 2 well past the points of interest. For each read we ran 75 cycles.
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