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332 results • Page
1 of 7
Sort: Votes
Rank
Views
Votes
Replies
9
votes
15
replies
816
views
Construction of single sequence assembly out of contigs
Contigs
Bacteria
Genome
WGS
6 days ago by
analyst
▴ 10
8
votes
6
replies
613
views
How to create a Venn Diagram for overlapping SVs from a merged VCF
truvari
structural-variants
r
vcf
venn-diagram
28 days ago by
Matteo Ungaro
▴ 70
6
votes
3
replies
249
views
How can I adjust Y-axis scale when making relative abundance box plot ?
statistics
box-plot
R
scale_adjustment
logarithm
updated 5 days ago by
Jeremy
▴ 860 • written 5 days ago by
ohtang7
▴ 40
5
votes
3
replies
340
views
Strand bias in supplementary alignments from Nanopore
minimap2
nanopore
strand
updated 27 days ago by
cmdcolin
★ 3.4k • written 27 days ago by
dariober
14k
5
votes
2
replies
254
views
RNA Contamination Tool for Developing Cell Samples
contamination
scRNA
quality
RNA
SoupX
10 days ago by
Rafael Soler
★ 1.2k
4
votes
6
replies
416
views
bwa mem hangs after a few thousand reads
bwa-mem
alignment
bwa
calling
variant
5 days ago by
cee28
▴ 30
4
votes
9
replies
708
views
Snakemake issue with wrappers
Python
Snakemake
27 days ago by
Begonia_pavonina
▴ 120
4
votes
6
replies
402
views
Unexpected separation of RNA-seq samples on PCA plot
depletion
PCA
rRNA
plot
RNA-seq
14 days ago by
Tihana
▴ 10
4
votes
7
replies
563
views
SNP IDs
SNP
19 days ago by
kl
▴ 10
3
votes
1
reply
201
views
KEGG DATABASE
DATABASE
KEGG
updated 2 days ago by
Mensur Dlakic
★ 25k • written 2 days ago by
Sijjil
• 0
3
votes
3
replies
299
views
How to proceed after Kraken2 analysis
rnaseq
kraken
updated 26 days ago by
dthorbur
▴ 890 • written 27 days ago by
pixie@bioinfo
★ 1.5k
3
votes
4
replies
430
views
Downstream analysis with DEseq2 normalization
DEseq2
integration
15 days ago by
QX
• 0
3
votes
7
replies
583
views
IGV not showing bigwig track information
bigwig
IGV
ChIP-seq
updated 20 days ago by
ATpoint
78k • written 24 days ago by
Rory Osborne
▴ 10
3
votes
6
replies
450
views
scRNA-seq: Consistent low number of cells and low fraction reads across the samples
scRNA-seq
cells
mRNA
expression
gene
updated 3 days ago by
jv
★ 1.2k • written 5 days ago by
newbee
▴ 40
3
votes
9
replies
1.6k
views
How to get negative training set if I don't know what constitutes negative?
machine-learning
dna-sequence
blast
updated 28 days ago by
Ram
41k • written 7.2 years ago by
nafizh
• 0
3
votes
4
replies
319
views
Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not present in R
FDR
volcano
plotting
R
plot
updated 6 days ago by
Nitin Narwade
★ 1.5k • written 6 days ago by
RNAseqer
▴ 250
3
votes
2
replies
249
views
t-test by row
R
t-test
updated 12 days ago by
dthorbur
▴ 890 • written 13 days ago by
sooni
▴ 10
2
votes
6
replies
2.1k
views
No best K value found
Assembly
Kmergenie
updated 10 days ago by
shaileshdesai76
• 0 • written 6.8 years ago by
kspata
▴ 80
2
votes
4
replies
401
views
What are the steps for Germline and Somatic CNV detection using CNVkit?
cnv
cnvkit
16 days ago by
ahmad mousavi
▴ 770
2
votes
3
replies
319
views
Selecting a subset of MSigDB database for GSEA
fgsea
clusterprofiler
GSEA
18 days ago by
Orange
▴ 10
2
votes
6
replies
472
views
Burrows-Wheeler transform
Python
BWT
DNA
updated 21 days ago by
Ram
41k • written 22 days ago by
Balqees
• 0
2
votes
2
replies
139
views
4 Fastq files for a single run generated by 10X
scRNA-Seq
Fastq
SRA
10X
20 minutes ago by
hkarakurt
▴ 180
2
votes
2
replies
306
views
DESeq2 installation failures
DEseq2
updated 15 days ago by
Michael
53k • written 17 days ago by
dantuluri
• 0
2
votes
2
replies
594
views
6 follow
Why runing scDblFinder before and after removing low QC cells gives different results
singleCellExperiment
scDblFinder
SMART-Seq
updated 7 days ago by
e.r.zakiev
▴ 170 • written 5 months ago by
Assa Yeroslaviz
★ 1.8k
2
votes
2
replies
241
views
Compare similarity of protein variants
protein
structure
updated 18 days ago by
dthorbur
▴ 890 • written 19 days ago by
GP
• 0
2
votes
1
reply
165
views
unicycler error : [Errno 13] Permission denied:
unicycler
updated 6 days ago by
barslmn
★ 2.0k • written 7 days ago by
jiyoung
▴ 20
2
votes
3
replies
445
views
How to check if my sequence is DNA or Protein in BioPython?
genomics
biopython
fasta
updated 22 days ago by
Joe
21k • written 24 days ago by
O.rka
▴ 710
2
votes
11
replies
683
views
Data preparation for a ML model
machine-learning
RNA-Seq
R
python
biomarkers
4 days ago by
sil_bioinfo
▴ 40
2
votes
9
replies
685
views
Salmon (or other pseudo-mappers) for multi-species RNAseq read filtering
STAR
Salmon
mapper
aligner
RNAseq
5 days ago by
ian.will
▴ 10
2
votes
5
replies
211
views
kallisto index build difference according to version
index
version
kallisto
updated 21 hours ago by
dsull
★ 5.1k • written 1 day ago by
estilo
• 0
2
votes
6
replies
502
views
Annotating genome based on Sequence
genome
annotation
updated 26 days ago by
Darked89
4.5k • written 5 weeks ago by
buhbs
▴ 10
2
votes
2
replies
289
views
Wrong in Deeptools : the enrichment of TSS and TES region are similar when using scale-region
plotprofile
computematrix
Deeptools
scale-region
11 days ago by
hao
▴ 10
2
votes
5
replies
706
views
Pre-processing for Agilent microarray data?
affymetrix
microarray
gene
agilent
rna
updated 18 days ago by
1769mkc
★ 1.1k • written 6 months ago by
survive
• 0
2
votes
2
replies
819
views
Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when pivoting from wide to long format
rnaseq
pivot_longer
ggplot2
updated 6 days ago by
cmdcolin
★ 3.4k • written 6 days ago by
Dylan C-C
• 0
2
votes
1
reply
247
views
EnhancedVolcano underrepresenting DEGs
R
updated 6 days ago by
Kevin Blighe
86k • written 8 days ago by
jabbari.parnian
▴ 30
2
votes
1
reply
161
views
Extract variants from 100 000 genomes project
variants
100000-genomes-project
updated 14 days ago by
Ram
41k • written 14 days ago by
Mairena
• 0
2
votes
5
replies
361
views
kraken2 bacteria database 250GB+
metagenomics
16s
kraken2
kraken
updated 26 days ago by
GenoMax
136k • written 26 days ago by
10mz1
• 0
2
votes
2
replies
212
views
R script in docker
R
Visual_studio_code
Docker
4 days ago by
mrashad
▴ 70
1
vote
1
reply
205
views
How to properly quantify gene expression of tandem duplicates from RNA-seq
pipeline
illumina
plants
RNA-seq
updated 21 days ago by
dthorbur
▴ 890 • written 22 days ago by
missTique
• 0
1
vote
4
replies
378
views
Efficient Bulk Data Retrieval from NCBI BioProject
ncbi
SRAtoolkit
prefetch
17 days ago by
George
• 0
1
vote
9
replies
619
views
Command line or python RNA-seq read simulator
simulation
RNA-seq
24 days ago by
i.sudbery
18k
1
vote
3
replies
281
views
Should unique gene names/transcript IDs be used for ribosomal gene copies in a GTF/GFF file?
GTF
GFF
updated 18 days ago by
dthorbur
▴ 890 • written 20 days ago by
cyril-cros
▴ 940
1
vote
2
replies
365
views
Bulk RNAseq Salmon index building which transcriptome to use
Salmon
RNA-seq
26 days ago by
Orange
▴ 10
1
vote
0
replies
142
views
What are the methods to correlate/study metabolomics data to proteomics data?
metabolomics
proteomics
multiomics
12 days ago by
WUSCHEL
▴ 720
1
vote
3
replies
2.2k
views
BBMap : NH:i:1 and XT:A:R
bbmap
updated 12 days ago by
ayaosama2111
▴ 10 • written 7.1 years ago by
Nicolas Rosewick
10k
1
vote
0
replies
15
views
GEO dataset Microarray data analysis help
microarray
NCBI
GEO
R
data
1 hour ago by
Confused_human
▴ 20
1
vote
1
reply
206
views
Model matrix confront 2 groups out of 3
modelmatrix
r
designformula
deseq2
drimseq
updated 15 days ago by
ATpoint
78k • written 15 days ago by
dylannicoembros
• 0
1
vote
1
reply
181
views
RepeatModeler-2.0 BuildDatabase error
BuildDatabase
RepeatModeler
updated 19 days ago by
shelkmike
★ 1.1k • written 20 days ago by
1041853545
• 0
1
vote
2
replies
304
views
featureCounts error???
featureCounts
error
updated 22 days ago by
Gordon Smyth
★ 6.5k • written 23 days ago by
Samer
• 0
1
vote
4
replies
296
views
Deseq2 5 level condition - building contrast
rna-seq
deseq2
updated 13 days ago by
ATpoint
78k • written 13 days ago by
annaA
▴ 10
332 results • Page
1 of 7
Recent Votes
Comment: 4 Fastq files for a single run generated by 10X
Comment: 4 Fastq files for a single run generated by 10X
Answer: How do you generate TMM normalized counts using EdgeR?
The Biostar Handbook. A bioinformatics e-book for beginners.
GEO dataset Microarray data analysis help
C: Batch effects : ComBat or removebatcheffects (limma package) ?
Answer: Batch effects : ComBat or removebatcheffects (limma package) ?
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Recent Replies
Comment: Microarray batch correction method suggestions
by
ATpoint
78k
Makes no sense in my opinion. It's different experiments that cannot be quantitatively compared.
Comment: How to download multiple genome files using command line (MacOS) using datasets
by
scholaraspect2008
• 0
by means of that, how should i write my scripting? say i have GCF000001 GCF000002 GCF000003 btw sorry if i wasn't that clear with the …
Comment: 4 Fastq files for a single run generated by 10X
by
hkarakurt
▴ 180
Thank you for your detailed answer. I will check the reads and compare them with chemistry manual as you suggested. Thank you again for yo…
Comment: Microarray batch correction method suggestions
by
Sumeet
• 0
Thank you @atpoint for your response. However, aim of analysing to generate a matrix with all dataset available after batch correction.
Comment: what should I do if I get a compromised sample of scRNA-seq data?
by
ATpoint
78k
Agreed. I would just force the cells to 5000 or so, and then proceed with the normal QC. If there's a lot of trash "cells" in the dataset t…
Comment: How to download multiple genome files using command line (MacOS) using datasets
by
rj.rezwan
• 0
you should use the `wild cards` to download all the given above GCF files. Moverover, you can use the commands of `curl` , `wget` and `slow…
Comment: Microarray batch correction method suggestions
by
ATpoint
78k
This has been asked so many times before. Analyse them separately, then make a statement on reproducibility of results using a meta-analysi…
Comment: Microbial gene coverage from blast result
by
aanchal.yadav
• 0
What is qcovhsp (high scoring segment pair) in BLAST output. Can we use this parameter to calculate the gene coverage?
Answer: Best way to normalize transcript reads data for PCA & correlation and further bi
by
Jeremy
▴ 860
Scaling the data will give you Z-scores. This is a standard way of preparing data for PCA. I would also suggest trying a center-log-ratio…
Comment: How to resolve the error of protein lacking a stop codon when using GenomeThread
by
peanut
• 0
Thank you for your answer,but after verifying the protein file, it seems there is no problem. Even if there are missing codons, the program…
Comment: Help with gatk CreateSequenceDictionary
by
Chris
▴ 230
It worked! Thanks Matt!
Comment: Finding human .vcf files online to download
by
cmdcolin
★ 3.4k
i can't really tell you why your code doesn't work if you dont provide it. and, if you describe as much as possible what your goals are, th…
Answer: Help with gatk CreateSequenceDictionary
by
MatthewP
★ 1.3k
maybe try?: -R /variant_calling/Desktop/demo/supporting_files/hg38/hg38.fa -O /variant_calling/Desktop/demo/supporting_files/hg38/hg3…
Comment: Java error while running HiCDC overview code
by
Brian Bushnell
20k
Looks like you have corrupt or improperly-formatted input. It's expecting to parse a floating-point number where the word "score" appears.…
Comment: what should I do if I get a compromised sample of scRNA-seq data?
by
dsull
★ 5.1k
The knee plot is just one type of QC. I'd say just proceed with your analysis and see if you observe anything funky (analysis itself is a Q…
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