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84 results • Page
1 of 2
Sort: Votes
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Views
Votes
Replies
9
votes
15
replies
740
views
Construction of single sequence assembly out of contigs
Contigs
Bacteria
Genome
WGS
1 day ago by
analyst
▴ 10
5
votes
2
replies
242
views
RNA Contamination Tool for Developing Cell Samples
contamination
scRNA
quality
RNA
SoupX
6 days ago by
Rafael Soler
★ 1.2k
4
votes
6
replies
342
views
bwa mem hangs after a few thousand reads
bwa-mem
alignment
bwa
calling
variant
1 day ago by
cee28
▴ 30
3
votes
4
replies
287
views
Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not present in R
FDR
volcano
plotting
R
plot
updated 1 day ago by
Nitin Narwade
★ 1.5k • written 1 day ago by
RNAseqer
▴ 250
3
votes
3
replies
179
views
How can I adjust Y-axis scale when making relative abundance box plot ?
statistics
box-plot
R
scale_adjustment
logarithm
updated 19 hours ago by
Jeremy
▴ 840 • written 1 day ago by
ohtang7
▴ 40
2
votes
9
replies
646
views
Salmon (or other pseudo-mappers) for multi-species RNAseq read filtering
STAR
Salmon
mapper
aligner
RNAseq
23 hours ago by
ian.will
▴ 10
2
votes
2
replies
580
views
6 follow
Why runing scDblFinder before and after removing low QC cells gives different results
singleCellExperiment
scDblFinder
SMART-Seq
updated 3 days ago by
e.r.zakiev
▴ 170 • written 5 months ago by
Assa Yeroslaviz
★ 1.8k
2
votes
6
replies
2.1k
views
No best K value found
Assembly
Kmergenie
updated 6 days ago by
shaileshdesai76
• 0 • written 6.8 years ago by
kspata
▴ 80
2
votes
2
replies
198
views
scRNA-seq: Consistent low number of cells and low fraction reads across the samples
scRNA-seq
cells
mRNA
expression
gene
updated 8 hours ago by
ATpoint
78k • written 1 day ago by
newbee
▴ 40
2
votes
1
reply
153
views
unicycler error : [Errno 13] Permission denied:
unicycler
updated 2 days ago by
barslmn
★ 2.0k • written 2 days ago by
jiyoung
▴ 20
2
votes
2
replies
159
views
R script in docker
R
Visual_studio_code
Docker
6 hours ago by
mrashad
▴ 70
2
votes
1
reply
232
views
EnhancedVolcano underrepresenting DEGs
R
updated 2 days ago by
Kevin Blighe
86k • written 4 days ago by
jabbari.parnian
▴ 30
2
votes
11
replies
658
views
Data preparation for a ML model
machine-learning
RNA-Seq
R
python
biomarkers
5 hours ago by
sil_bioinfo
▴ 30
2
votes
2
replies
557
views
Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when pivoting from wide to long format
rnaseq
pivot_longer
ggplot2
updated 1 day ago by
cmdcolin
★ 3.4k • written 1 day ago by
Dylan C-C
• 0
1
vote
6
replies
329
views
Discrepancy in total number of bases in trimmed read1 and read2 files after BBDuk
bbduk
1 day ago by
CTLong
▴ 20
1
vote
6
replies
502
views
frequency plot for peaks
chip-seq
chipseeker
updated 1 day ago by
Ankit
▴ 400 • written 17 days ago by
Mehwish
▴ 10
1
vote
4
replies
261
views
Bowtie mapping for single_end read
bowtie
2 days ago by
Rita
• 0
1
vote
0
replies
93
views
Visualize and explore eventalign data against reference
igv
minimap
nanopolish
nanopore
ngs
3 days ago by
joe
▴ 390
1
vote
3
replies
253
views
Identify clusters of populations based on gene expression
Seq
Single
cell
RNA
updated 2 days ago by
Nitin Narwade
★ 1.5k • written 2 days ago by
Bine
▴ 50
1
vote
1
reply
182
views
Match variants for allele frequency, LD score, and other features
snp
1 day ago by
Jautis
▴ 520
1
vote
2
replies
190
views
Problem in installing 'magick' R package
R
installation
package
magick
updated 1 day ago by
DBScan
▴ 210 • written 1 day ago by
applepie
• 0
1
vote
1
reply
158
views
Harmony integration PC variance explained
scRNA
integration
harmony
updated 1 day ago by
CTLong
▴ 20 • written 3 days ago by
e.iich
• 0
1
vote
1
reply
158
views
Beginner differential methylation analysis
Methylation
updated 3 days ago by
Basti
★ 1.8k • written 4 days ago by
a.basitkhan1990
▴ 30
1
vote
4
replies
298
views
Analyze with Geo2R
R
NCBI
6 days ago by
anasjamshed
▴ 120
1
vote
1
reply
525
views
fragments.tsv.gz file in ATAC seq
ATAC-seq
updated 4 days ago by
tingting
▴ 10 • written 7 months ago by
Chris
▴ 230
1
vote
2
replies
188
views
How can I amend the output of a DIAMOND python script?
Python
Diamond
COG_analysis
14 hours ago by
eamaunders
• 0
0
votes
0
replies
105
views
How to find node Postion and source(sample) ?
vg
1 day ago by
zhang yi xing
▴ 20
0
votes
2
replies
1.4k
views
AttributeError: module 'collections' has no attribute 'Hashable'
Spades
updated 1 day ago by
jiyoung
▴ 20 • written 7 months ago by
Hayler Edu
▴ 30
0
votes
1
reply
151
views
How to create a mutation frequency comparison plot?
R
data-visualization
plot
updated 1 day ago by
rpolicastro
12k • written 1 day ago by
saipra003
▴ 10
0
votes
0
replies
77
views
GMT file from eggnog annotation
gmt
annotation
Eggnog
1 day ago by
jorge.cortes.miranda
• 0
0
votes
0
replies
90
views
sequencing deep mutational scanning library
mutagenesis
illumina
long-read
sequencing
1 day ago by
reaset41
• 0
0
votes
0
replies
91
views
Population study based on metaT and MetaG
metagenome
metatranscriptome
study
population
updated 1 day ago by
GenoMax
136k • written 1 day ago by
PierreGT
• 0
0
votes
1
reply
341
views
How to use conumee segment mean for gistic input
genomics
gistic
NGS
methylation
conumee
updated 1 day ago by
sativus
▴ 10 • written 14 months ago by
Thind amarinder
▴ 340
0
votes
0
replies
79
views
Conumee output as input for Gistic2.0
cnv
copy
gistic
cna
conumee
updated 1 day ago by
GenoMax
136k • written 1 day ago by
sativus
▴ 10
0
votes
0
replies
128
views
Mapping Mouse RNAseq Marker Genes to Reactome Pathways
single-cell
pathways
reactome
RNAseq
gene
1 day ago by
el24
▴ 40
0
votes
0
replies
88
views
deeptools k-means clustering
heatmap
deeptools
chipseq
1 day ago by
biology_inform
▴ 50
0
votes
0
replies
71
views
CHIPSEQ Analysis , DiffBind Parameters
DiffBind
ChIP-seq
1 day ago by
DINESHR
• 0
0
votes
4
replies
288
views
CHIPSEQ : Cut AND Run , DiffBind Parameters
Cut-Run
DiffBind
ChIP-seq
1 day ago by
DINESHR
• 0
0
votes
0
replies
78
views
GATK Mutect2 mouse dbSNP vcf files recommendations for mouse whole exome data
mouse
GATK
Mutect2
dbSNP
23 hours ago by
luckyday1661
• 0
0
votes
3
replies
254
views
Viral genes not showing up in combined mouse+virus alignment
RNAseq
22 hours ago by
cook.675
▴ 210
0
votes
1
reply
208
views
htShinyExample-5.3 - not working
htShiny
Oncoprint
InteractiveComplexHeatmap
updated 20 hours ago by
Ram
41k • written 6 days ago by
bioinfo
▴ 60
0
votes
0
replies
52
views
ADMIXTURE Freezes Right Before Completion
ADMIXTURE
admixture
14 hours ago by
maxlaubstein
• 0
0
votes
0
replies
59
views
how to calculate intramodular connectivity
WGCNA
intramodularConnectivity
12 hours ago by
hellokwmin
• 0
0
votes
3
replies
141
views
calculate nucleotide diversity from whole-genome-sequence data for individual genes
genomics
nucleotide_diversity
vcf
12 hours ago by
J
• 0
0
votes
1
reply
123
views
How to check for incorporation of plasmid DNA into human genomic DNA (ChIP-seq)?
plasmid
chipseq
updated 11 hours ago by
Nitin Narwade
★ 1.5k • written 1 day ago by
tss243
• 0
0
votes
2
replies
183
views
Cellcyclescoring did not work in Seurat V5
singlecell
updated 10 hours ago by
fracarb8
★ 1.3k • written 23 hours ago by
synat.keam
▴ 80
0
votes
4
replies
182
views
Can you help me to download list of miRNA from a SRA under a bioproject ?
bioproject
mirna
updated 8 hours ago by
ATpoint
78k • written 11 hours ago by
abourrieau
• 0
0
votes
1
reply
97
views
PAML Troubleshooting Help
PAML
codeml
updated 6 hours ago by
dthorbur
▴ 880 • written 11 hours ago by
sebabiokr
▴ 10
0
votes
0
replies
40
views
Should I scale all genes in single cell Seurat?
singlecell
4 hours ago by
synat.keam
▴ 80
0
votes
3
replies
148
views
In what case there are RR reads but no LL reads when detect inversions using IGV?
IGV
inversion
updated 4 hours ago by
Istvan Albert
99k • written 8 hours ago by
Jingfang
• 0
84 results • Page
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Answer: Bulk and Single Cell RNA-seq online course
Answer: Is there a need to batch correct FPKM or TPM values for within sample comparison
A: RNA-Seq post-DGE "Diagnostic tests"
Comment: p-value combination methods
Comment: p-value combination methods
Answer: Which Tools do you use for (Tandem) Repeat Detection? Why?
C: Run Makeblastdb For Compressed File
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Answer: Bulk and Single Cell RNA-seq online course
by
swbarnes2
13k
I'd start by getting tutorials for R libraries like DESeq, EdgeR, Seurat, etc, and learn by doing.
Answer: gene set enrichment analysis- by enrichGO
by
Istvan Albert
99k
Some analyses compare a subset of genes to a background. In those cases you would need to select a subset via some attributes like pvalues …
Comment: Ipyrad de novo for variant calling
by
Betsy
• 0
Were you ever able to resolve this error? I am having the exact same problem trying to run ipyrad on already demultiplexed fq.gz files
Comment: Is there a need to batch correct FPKM or TPM values for within sample comparison
by
ATpoint
78k
Depends on the analysis. If you do some sort of gene ratio calculation then probably yes. Batch correction does not affect all genes equall…
Answer: WGCNA tutorial docs needed: Horvath Lab site down
by
Rebecca
• 0
If there is a copy of the wgcna pdfs available please let me know!
Comment: How to filter .fasta file based on conditional statement
by
Brian Bushnell
19k
You're using BBTools v39.01. I just added the new flag in 39.06 :)
Answer: Where do these snpeff annotation come from?
by
Istvan Albert
99k
in principle you can do a snpeff dump hg38 that will generate a text output of the content of the database. in practice when I …
Comment: Can FPKM be used to create bar graphs for DEGs?
by
junli1988
• 0
LOL...It's a CSV file, and that's all I have in the folder. I agree that it is indeed the stuff of nightmares. But what can I do? It's not …
Answer: Is there a need to batch correct FPKM or TPM values for within sample comparison
by
jv
★ 1.2k
My assumption is that intra-sample comparisons should not require batch effect correction.
Comment: Tools or R / Python packages to perfom ML models
by
Michael
53k
If you have a lot of training data with class labels, as your dataset seems to be you could turn it into an ML classification problem. Gene…
Comment: p-value combination methods
by
Istvan Albert
99k
https://www.biostars.org/u/41501/ please don't delete post that have additional content associated with them having assistance from the C…
Comment: In what case there are RR reads but no LL reads when detect inversions using IGV
by
Istvan Albert
99k
I think a view as pairs is much cleaner as it shows the actual pairing and how they cross the gap. In the view you show it is not clear whe…
Answer: Extracting only soft/hard clipped reads from a bam file
by
Pierre Lindenbaum
158k
only soft clipped reads (but should be ok in most cases, as in bwa only secondary reads are hard clipped): samtools view -O BAM -o ou…
Comment: In what case there are RR reads but no LL reads when detect inversions using IGV
by
Jingfang
• 0
Thanks for your reply. The IGV image I show used color alignments by pair orientation, and view mate region in split screen. Blue reads …
Answer: Extracting only soft/hard clipped reads from a bam file
by
horeyezonr
▴ 10
Hi I know it was more than a year, but I'll just leave the answer here maybe it will help someone. With the modified code of yours, th…
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