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324 results • Page
1 of 7
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Rank
Views
Votes
Replies
0
votes
0
replies
6
views
bwa mem hangs after a few thousand reads
bwa-mem
alignment
bwa
calling
variant
14 minutes ago by
cee28
• 0
0
votes
1
reply
30
views
How to get unaligned reads and aligned reads into separate files from SAM/BAM?
bam
sam
reads
fastq
updated 36 minutes ago by
rpolicastro
12k • written 1 hour ago by
O.rka
▴ 710
0
votes
2
replies
68
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 2 hours ago by
Dylan C-C
• 0
1
vote
3
replies
94
views
Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not present in R
FDR
volcano
plotting
R
plot
updated 30 minutes ago by
dsull
★ 5.0k • written 4 hours ago by
RNAseqer
▴ 250
0
votes
1
reply
71
views
CHIPSEQ : Cut AND Run , DiffBind Parameters
Cut-Run
ChIP-seq
DiffBind
updated 1 hour ago by
GenoMax
136k • written 4 hours ago by
DINESHR
• 0
0
votes
0
replies
51
views
scVelo cell transitions from marker gene expressing cells
velocity
scvelo
RNA
8 hours ago by
rbronste
▴ 420
1
vote
3
replies
192
views
Identify clusters of populations based on gene expression
Seq
Single
cell
RNA
updated 7 hours ago by
Nitin Narwade
★ 1.5k • written 15 hours ago by
Bine
▴ 50
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 13 hours ago by
barslmn
★ 2.0k • written 15 hours ago by
Saurabh
• 0
0
votes
1
reply
117
views
Discrepancy in total number of bases in trimmed read1 and read2 files after BBDuk
bbduk
updated 13 hours ago by
GenoMax
136k • written 16 hours ago by
GeneBC12
• 0
2
votes
1
reply
110
views
unicycler error : [Errno 13] Permission denied:
unicycler
updated 13 hours ago by
barslmn
★ 2.0k • written 17 hours ago by
jiyoung
▴ 20
0
votes
0
replies
60
views
Does breadth of coverage signify expression?
Coverage
breadth
Bedtools
Expression
count
18 hours ago by
Smriti
▴ 10
1
vote
4
replies
210
views
Bowtie mapping for single_end read
bowtie
8 hours ago by
Rita
• 0
0
votes
0
replies
62
views
Viral genes not showing up in combined mouse+virus alignment
RNAseq
19 hours ago by
cook.675
▴ 200
0
votes
0
replies
62
views
String App in Cytoscape
App
String
cytoscape
23 hours ago by
hellokwmin
• 0
0
votes
0
replies
79
views
missing region in the process of annotation
annotatr
minfi
1 day ago by
Aki
▴ 10
1
vote
0
replies
75
views
Visualize and explore eventalign data against reference
igv
minimap
nanopolish
nanopore
ngs
1 day ago by
joe
▴ 390
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
9
votes
16
replies
659
views
Construction of single sequence assembly out of contigs
Contigs
Bacteria
Genome
WGS
4 hours ago by
analyst
▴ 10
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
232
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
0
replies
92
views
addPatternDensity to qsea object
maxDensityPattern
medip
qsea
1 day ago by
Jaykishan
• 0
0
votes
0
replies
98
views
Harmony integration PC variance explained
scRNA
integration
harmony
1 day ago by
e.iich
• 0
0
votes
3
replies
210
views
merged rs number information
merged
dbsnp
22 hours ago by
sskimvd
• 0
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
2
votes
1
reply
221
views
EnhancedVolcano underrepresenting DEGs
R
updated 12 hours ago by
Kevin Blighe
86k • written 2 days ago by
jabbari.parnian
▴ 30
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
0
replies
114
views
Negative F statistics for sex check in plink
plink
check
sex
2 days ago by
kl
▴ 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
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
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
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
3
replies
295
views
Annovar - Annotated file cells show string
annovar
4 days ago by
Roshan
• 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
0
replies
153
views
htShinyExample-5.3 - not working
htShiny
Oncoprint
InteractiveComplexHeatmap
4 days ago by
bioinfo
▴ 60
0
votes
0
replies
154
views
Seeking Advice on WGCNA for Nematode Sexual Dimorphism
WGCNA
Worms
RNA-Seq
4 days ago by
kdca
• 0
0
votes
3
replies
265
views
labelling the clusters from the CD4 T cell scRNAseq data
scRNAseq
4 days ago by
Sara
▴ 230
0
votes
0
replies
790
views
Any tools for finding the telomere sequences / lengths directly for nanopore sequencing reads without any prior knowledge of the organism
genomics
telomeres
reads
4 days ago by
Mark
• 0
0
votes
0
replies
148
views
not best k value found
de
assemblly
assembly
novo
kmergenie
4 days ago by
shaileshdesai76
• 0
0
votes
0
replies
158
views
Multi-mapped reads in Ribo-Seq data, discard or keep?
STAR
ribo-seq
multi-mapped
rna-seq
TE
5 days ago by
Carmen
• 0
0
votes
0
replies
163
views
Identifying differentially expressed loci for gene duplicates using DESeq2
rna-seq
deseq2
5 days ago by
pl23
• 0
0
votes
2
replies
271
views
Find Genes in Homer Analysis that have the enriched Motif
single
ORA
nucleus
mRNA
Homer
18 hours ago by
je71xusa
• 0
0
votes
2
replies
257
views
Tool to get genes in the neighbourhood of a particular gene
locus
Gene
updated 5 days ago by
Raony Guimarães
★ 1.3k • written 5 days ago by
ThePlaintiff
▴ 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
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
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
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
0
votes
3
replies
279
views
R ComplexHeatmap - Dividing Column Annotation into Distinct Y-Axis Scales
R
complexheatmap
updated 6 hours ago by
jv
★ 1.2k • written 6 days ago by
TC_Chang
▴ 10
0
votes
0
replies
106
views
Find equivalent pathways between KEGG, Reactome, and WikiPathways
pathway
mapping
database
6 days ago by
Ngrin
• 0
0
votes
0
replies
116
views
GenAlEx Haploid Data Detecting Recombination
GenAlEx
Popgen
Haploid
Recombination
6 days ago by
turcoa1
• 0
0
votes
0
replies
123
views
TF Footprinting using HINT ATAC module from RGT
hintatac
footprinting
rgttoolbox
atacseq
6 days ago by
alphaflylizard
• 0
324 results • Page
1 of 7
Recent Votes
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?
Extract UMIs using UMI-tools
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Recent Awards •
All
Popular Question
to
O.rka
▴ 710
Popular Question
to
Daniel
▴ 30
Popular Question
to
prasundutta87
▴ 660
Popular Question
to
RNAseqer
▴ 250
Scholar
to
Devon Ryan
104k
Scholar
to
Pierre Lindenbaum
158k
Teacher
to
Trivas
★ 1.5k
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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