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73 results • Page
1 of 2
Sort: Votes
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Votes
Replies
9
votes
16
replies
662
views
Construction of single sequence assembly out of contigs
Contigs
Bacteria
Genome
WGS
4 hours ago by
analyst
▴ 10
5
votes
2
replies
235
views
RNA Contamination Tool for Developing Cell Samples
contamination
scRNA
quality
RNA
SoupX
4 days ago by
Rafael Soler
★ 1.2k
3
votes
2
replies
231
views
t-test by row
R
t-test
updated 6 days ago by
dthorbur
▴ 860 • written 6 days ago by
sooni
▴ 10
2
votes
2
replies
569
views
6 follow
Why runing scDblFinder before and after removing low QC cells gives different results
singleCellExperiment
scDblFinder
SMART-Seq
updated 1 day 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 4 days ago by
shaileshdesai76
• 0 • written 6.8 years ago by
kspata
▴ 80
2
votes
8
replies
578
views
Salmon (or other pseudo-mappers) for multi-species RNAseq read filtering
STAR
Salmon
mapper
aligner
RNAseq
updated 1 day ago by
GenoMax
136k • written 7 days ago by
ian.will
▴ 10
2
votes
1
reply
110
views
unicycler error : [Errno 13] Permission denied:
unicycler
updated 14 hours ago by
barslmn
★ 2.0k • written 18 hours ago by
jiyoung
▴ 20
2
votes
1
reply
221
views
EnhancedVolcano underrepresenting DEGs
R
updated 13 hours ago by
Kevin Blighe
86k • written 2 days ago by
jabbari.parnian
▴ 30
1
vote
3
replies
192
views
Identify clusters of populations based on gene expression
Seq
Single
cell
RNA
updated 8 hours ago by
Nitin Narwade
★ 1.5k • written 15 hours ago by
Bine
▴ 50
1
vote
6
replies
457
views
frequency plot for peaks
chip-seq
chipseeker
updated 1 hour ago by
Ankit
▴ 400 • written 15 days ago by
Mehwish
▴ 10
1
vote
1
reply
838
views
cellphonedb results visualization
cellphonedb
ktplotspy
cpdb
visulization
updated 6 days ago by
miguellarrazlopezdenovales
▴ 20 • written 10 months ago by
piotto
▴ 20
1
vote
3
replies
102
views
Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not present in R
FDR
volcano
plotting
R
plot
updated 1 hour ago by
dsull
★ 5.0k • written 4 hours ago by
RNAseqer
▴ 250
1
vote
4
replies
290
views
Analyze with Geo2R
R
NCBI
4 days ago by
anasjamshed
▴ 120
1
vote
0
replies
75
views
Visualize and explore eventalign data against reference
igv
minimap
nanopolish
nanopore
ngs
1 day ago by
joe
▴ 390
1
vote
0
replies
134
views
What are the methods to correlate/study metabolomics data to proteomics data?
metabolomics
proteomics
multiomics
5 days ago by
WUSCHEL
▴ 720
1
vote
2
replies
190
views
DOES MGI SEQUENCING RESULT CONTAINS MULTIPLE FILES FOR SINGLE SAMPLE
whole
genome
assembly
sequencing
updated 5 days ago by
WouterDeCoster
47k • written 5 days ago by
manaswiniparija3
▴ 10
1
vote
1
reply
515
views
fragments.tsv.gz file in ATAC seq
ATAC-seq
updated 2 days ago by
tingting
▴ 10 • written 7 months ago by
Chris
▴ 230
1
vote
2
replies
280
views
Wrong in Deeptools : the enrichment of TSS and TES region are similar when using scale-region
plotprofile
computematrix
Deeptools
scale-region
5 days ago by
hao
• 0
1
vote
1
reply
225
views
Eigen_phred_coding values interpretation
variation
SNP
annotation
6 days ago by
Lukas
▴ 40
1
vote
1
reply
147
views
Beginner differential methylation analysis
Methylation
updated 1 day ago by
Basti
★ 1.8k • written 2 days ago by
a.basitkhan1990
▴ 30
1
vote
4
replies
210
views
Bowtie mapping for single_end read
bowtie
9 hours ago by
Rita
• 0
1
vote
3
replies
2.2k
views
BBMap : NH:i:1 and XT:A:R
bbmap
updated 6 days ago by
ayaosama2111
▴ 10 • written 7.0 years ago by
Nicolas Rosewick
10k
0
votes
0
replies
221
views
The number of variations in the pan-genome is reduced compared to the variations in the input VCF file
vg
4 days ago by
Wenke
• 0
0
votes
1
reply
230
views
MinKNOW software installation doubt for MinION Nanopore sequencing
MinKNOW
MinION
Nanopore
updated 3 days ago by
GenoMax
136k • written 4 days ago by
Soumajit
▴ 40
0
votes
3
replies
331
views
Alternatives to Music2 for rnaseq deconvolution without disease scRNA dataset
scRNA
deconvolution
Music
Music2
bulk
updated 3 days ago by
ATpoint
78k • written 4 days ago by
manuelmourato25
• 0
0
votes
1
reply
233
views
issue in RNA -seq analysis
NGS
RNA-Seq
updated 3 days ago by
GenoMax
136k • written 3 days ago by
subhiksha
• 0
0
votes
0
replies
114
views
Negative F statistics for sex check in plink
plink
check
sex
2 days ago by
kl
▴ 10
0
votes
0
replies
102
views
[maftools]Too many multi_hit and missense mutation
maftools
gatk
MAF
data
WES
VCF
2 days ago by
jiazheng_lin
• 0
0
votes
3
replies
1.0k
views
Error with Ice normalization when running HiC-Pro
Hi-C
HiChIP
HiC-Pro
updated 2 days ago by
Cibo
• 0 • written 2.0 years ago by
Amina
• 0
0
votes
0
replies
98
views
Harmony integration PC variance explained
scRNA
integration
harmony
1 day ago by
e.iich
• 0
0
votes
0
replies
92
views
addPatternDensity to qsea object
maxDensityPattern
medip
qsea
1 day ago by
Jaykishan
• 0
0
votes
0
replies
85
views
Differentiate sequenced and imputed variants in BGEN files
imputation
bgen
ukb
1 day ago by
user230613
▴ 350
0
votes
4
replies
233
views
Species coverage in the NCBI protein NR database ?
NR
updated 1 day ago by
Istvan Albert
99k • written 1 day ago by
HERMAN
▴ 10
0
votes
1
reply
180
views
Chipseq peak calling and peak frequency region
chipseeker
macs2
updated 1 day ago by
Arup Ghosh
3.2k • written 3 days ago by
Mehwish
▴ 10
0
votes
2
replies
194
views
how to use pilon
genome
pipelines
assembly
pilon
contig
updated 1 day ago by
Arup Ghosh
3.2k • written 6 days ago by
vasudhapai
• 0
0
votes
0
replies
79
views
missing region in the process of annotation
annotatr
minfi
1 day ago by
Aki
▴ 10
0
votes
0
replies
62
views
String App in Cytoscape
App
String
cytoscape
1 day ago by
hellokwmin
• 0
0
votes
3
replies
210
views
merged rs number information
merged
dbsnp
23 hours ago by
sskimvd
• 0
0
votes
0
replies
62
views
Viral genes not showing up in combined mouse+virus alignment
RNAseq
20 hours ago by
cook.675
▴ 200
0
votes
0
replies
61
views
Does breadth of coverage signify expression?
Coverage
breadth
Bedtools
Expression
count
19 hours ago by
Smriti
▴ 10
0
votes
2
replies
271
views
Find Genes in Homer Analysis that have the enriched Motif
single
ORA
nucleus
mRNA
Homer
19 hours ago by
je71xusa
• 0
0
votes
1
reply
103
views
Python function to export the annotated records to genbank file using python and biopython
biopython
python
bioinformatic
programming
updated 14 hours ago by
barslmn
★ 2.0k • written 16 hours ago by
Saurabh
• 0
0
votes
4
replies
217
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
RNA-Seq
Nanopore
ONT
differential
expression
9 hours ago by
tw_140
• 0
0
votes
0
replies
51
views
scVelo cell transitions from marker gene expressing cells
velocity
scvelo
RNA
9 hours ago by
rbronste
▴ 420
0
votes
3
replies
279
views
R ComplexHeatmap - Dividing Column Annotation into Distinct Y-Axis Scales
R
complexheatmap
updated 7 hours ago by
jv
★ 1.2k • written 6 days ago by
TC_Chang
▴ 10
0
votes
2
replies
82
views
Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when pivoting from wide to long format
rnaseq
pivot_longer
ggplot2
updated 2 hours ago by
cmdcolin
★ 3.4k • written 3 hours ago by
Dylan C-C
• 0
0
votes
1
reply
40
views
How to get unaligned reads and aligned reads into separate files from SAM/BAM?
bam
sam
reads
fastq
updated 1 hour ago by
rpolicastro
12k • written 2 hours ago by
O.rka
▴ 710
0
votes
0
replies
10
views
bwa mem hangs after a few thousand reads
bwa-mem
alignment
bwa
calling
variant
45 minutes ago by
cee28
• 0
0
votes
0
replies
4
views
MUSCLE Protein Alignment of Distantly Related Proteins
muscle
protein
alignment
10 minutes ago by
Richard Fontaine
• 0
0
votes
0
replies
1
view
How to find node Postion and source(sample) ?
vg
just now by
zhang yi xing
▴ 20
73 results • Page
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Recent Votes
Comment: SPAdes error: finished abnormally, OS return value: 21
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
Comment: unicycler error : [Errno 13] Permission denied:
Comment: unicycler error : [Errno 13] Permission denied:
Answer: SPAdes error: finished abnormally, OS return value: 21
Comment: SPAdes error: finished abnormally, OS return value: 21
Removing UMI with UMI tools?
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Recent Replies
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
by
dsull
★ 5.0k
Yeah, sometimes it looks "prettier" to plot p-value rather than adjusted p-value; although either one is technically ok to plot (even multi…
Comment: How to get unaligned reads and aligned reads into separate files from SAM/BAM?
by
rpolicastro
12k
I suppose if you really wanted to do it in one pass pysam would be an option. Courtesy of ChatGPT with a few modifications, and tested to s…
Comment: frequency plot for peaks
by
Ankit
▴ 400
what is your txdb? can you explain your experiment in detail?
Comment: Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when
by
cmdcolin
★ 3.4k
paste the file in csv format and a R wizard might come along and help :)
Comment: Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when
by
rpolicastro
12k
Your intuition was correct. You want to make two separate data frames and join them on sample name. This code is untested but will probably…
Comment: Generate Read counts from bam file
by
ATpoint
78k
It has nothing to do with low complexity. You always map to the entire genome since the reads can come from the entire genome. If you take …
Comment: CHIPSEQ : Cut AND Run , DiffBind Parameters
by
ATpoint
78k
DiffBind uses DESeq2 for differential analysis and its method to moderate logFCs. When noise is high and there is little evidence for diffe…
Comment: p-value combination methods
by
dsull
★ 5.0k
Was this response written by a LLM? It's a useful response but it doesn't really answer the initial question... In response to the OP ques…
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
by
RNAseqer
▴ 250
Well, because I want to also draw attention to nominally significant genes as they are subjected to follow up experiments and would be nice…
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
by
Nitin Narwade
★ 1.5k
Actually, to add an **EXACT line/mark** for one value based on another is impossible (for me at least). What you can do is, select the min…
Comment: Construction of single sequence assembly out of contigs
by
analyst
▴ 10
Thanks colindaven!
Comment: Generate Read counts from bam file
by
Enrique
• 0
Great appreciation. If you don't use restrictive arguments in the mapping, is better to use the entire genome to avoid the false positives …
Comment: Generate Read counts from bam file
by
ATpoint
78k
No, absolutely not. Mapping to such a tiny subset leads to false positives. Use the entire genome that includes the mt reference.
Answer: Generate Read counts from bam file
by
Enrique
• 0
Hello, I recommend you using the mitochondrial reference genome. For the GTF file (or GFF, they are in general the same), checkout this pos…
Comment: How to deeply sequence long inserts
by
Brian Bushnell
19k
Merging paired reads is a good idea. Then you get nice, long reads... and actually, as long as you have enough coverage, you can just mer…
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