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75 results • Page
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123
views
TF Footprinting using HINT ATAC module from RGT
hintatac
footprinting
rgttoolbox
atacseq
5 days ago by
alphaflylizard
• 0
0
votes
0
replies
116
views
GenAlEx Haploid Data Detecting Recombination
GenAlEx
Popgen
Haploid
Recombination
5 days ago by
turcoa1
• 0
0
votes
0
replies
105
views
Find equivalent pathways between KEGG, Reactome, and WikiPathways
pathway
mapping
database
5 days ago by
Ngrin
• 0
1
vote
0
replies
132
views
What are the methods to correlate/study metabolomics data to proteomics data?
metabolomics
proteomics
multiomics
5 days ago by
WUSCHEL
▴ 720
0
votes
0
replies
163
views
Identifying differentially expressed loci for gene duplicates using DESeq2
rna-seq
deseq2
4 days ago by
pl23
• 0
0
votes
0
replies
156
views
Multi-mapped reads in Ribo-Seq data, discard or keep?
STAR
ribo-seq
multi-mapped
rna-seq
TE
4 days ago by
Carmen
• 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
769
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
153
views
Seeking Advice on WGCNA for Nematode Sexual Dimorphism
WGCNA
Worms
RNA-Seq
4 days ago by
kdca
• 0
0
votes
0
replies
152
views
htShinyExample-5.3 - not working
htShiny
Oncoprint
InteractiveComplexHeatmap
4 days ago by
bioinfo
▴ 60
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
3 days ago by
Wenke
• 0
0
votes
0
replies
113
views
Negative F statistics for sex check in plink
plink
check
sex
2 days ago by
kl
▴ 10
0
votes
0
replies
101
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
87
views
Harmony integration PC variance explained
scRNA
integration
harmony
1 day ago by
e.iich
• 0
0
votes
0
replies
104
views
Interpretation of mean-variance trend in voom
EdgeR
Voom
updated 6 days ago by
Ram
41k • written 7 days ago by
Ivana
• 0
0
votes
0
replies
72
views
Differentiate sequenced and imputed variants in BGEN files
imputation
bgen
ukb
1 day ago by
user230613
▴ 350
1
vote
0
replies
62
views
Visualize and explore eventalign data against reference
igv
minimap
nanopolish
nanopore
ngs
19 hours ago by
joe
▴ 390
0
votes
0
replies
66
views
missing region in the process of annotation
annotatr
minfi
16 hours ago by
Aki
▴ 10
0
votes
0
replies
51
views
String App in Cytoscape
App
String
cytoscape
14 hours ago by
hellokwmin
• 0
0
votes
0
replies
48
views
Viral genes not showing up in combined mouse+virus alignment
RNAseq
10 hours ago by
cook.675
▴ 200
0
votes
0
replies
44
views
Does breadth of coverage signify expression?
Coverage
breadth
Bedtools
Expression
count
9 hours ago by
Smriti
▴ 10
0
votes
0
replies
41
views
How should I run ssgsea analysis ?
functional
TPM
enrichment
gsea
ssgsea
6 hours ago by
DareDevil
★ 3.3k
0
votes
0
replies
25
views
Comparing 3 Data Sets using DeSeq and Heatmaps
DeSeq
Normalization
1 hour ago by
harter-ainsworth.izaak
• 0
0
votes
0
replies
21
views
p-value combination methods
rnaseq
NB-GLM
p-value
meta-Analysis
1 hour ago by
sehriban.buyukkilic
• 0
0
votes
0
replies
30
views
How to deeply sequence long inserts
NGS
phage
read
display
Long
updated 23 minutes ago by
GenoMax
136k • written 2 hours ago by
Ryan
• 0
75 results • Page
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Recent Votes
Answer: Mapping quality in `vg giraffe`
Comment: Identify clusters of populations based on gene expression
Answer: How can I map coordinates between two strains of yeast?
Comment: Construction of single sequence assembly out of contigs
Answer: featureCounts results: low rate of 'Successfully assigned alignments'
The Biostar Herald for Monday, November 27, 2023
Comment: use bioservices.UniProt (python) to map uniprot accession to [multiple] ensembl
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Lila M
★ 1.2k
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Christian
▴ 30
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sehriban.buyukkilic
• 0
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joe_genome
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biohacker_tobe
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pixie@bioinfo
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doggie
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Recent Replies
Answer: Moving AF tag to new column in a VCF file
by
Pierre Lindenbaum
158k
extract the vcf as a tab delimited file, something like (not tested) bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%FORMAT/AF]\n' in…
Comment: How can I map coordinates between two strains of yeast?
by
GenoMax
136k
> genome sequences of two different strains of yeast Are they the same species?
Comment: How to do simple pathway analysis?
by
he1k
• 0
Hi [AK][1], I downloaded the KO.keg file. I was wondering what tool(s) you used to generate the "KO.tsv" file as you showed here. Thanks. …
Comment: How can I map coordinates between two strains of yeast?
by
dthorbur
▴ 840
I think that is an alternative to a synteny analysis, but I only know liftover in terms of annotations. OP asks for "coordinates between th…
Comment: Bowtie mapping for single_end read
by
ATpoint
78k
I am sceptical any tweaking of parameters will make a notable difference. Parameters in bowtie are very good at default, and given it's ChI…
Comment: How can I map coordinates between two strains of yeast?
by
cmdcolin
★ 3.4k
would something like liftover not be recommended? honest question
Comment: Best practices for differential expression analysis with low-yield Nanopore/ONT
by
dthorbur
▴ 840
That's good. But I still suspect this data might be really difficult to analyse. I have a handful of suggestions I would do to assess wheth…
Comment: Identify clusters of populations based on gene expression
by
dthorbur
▴ 840
One gene might not be enough data to "cluster" based on expression. Unless I'm missing something, that would just be breaking a single cont…
Comment: Best practices for differential expression analysis with low-yield Nanopore/ONT
by
tw_140
• 0
Yes, I performed ribosome depletion using an RNAse H based method.
Comment: Circular genome browser
by
cmdcolin
★ 3.4k
that's great to hear. one "proxy" for interactive is looking at the JS based tools, many are web based and interactive as a result. I have …
Comment: R ComplexHeatmap - Dividing Column Annotation into Distinct Y-Axis Scales
by
TC_Chang
▴ 10
Hi jv, Thank you for your reply. Basically, I'm trying to generate the figure shown below with two different y-axis scales. Any suggestio…
Comment: Best practices for differential expression analysis with low-yield Nanopore/ONT
by
dthorbur
▴ 840
I don't have a suggestion for low yield DE analyses, but I am curious about the samples. Did you conduct any ribo-depletion steps prior to …
Answer: How can I map coordinates between two strains of yeast?
by
dthorbur
▴ 840
It sounds like you are looking for synteny between the two genomes. I'm assuming they are assembled, but that may not be the case. If so, […
Comment: Identify clusters of populations based on gene expression
by
Nitin Narwade
★ 1.5k
Why don't you just plot it on your UMAP If it is specific to one cluster/sub-population you should get a relatively high expression in that…
Answer: The difference blastn output when using subject and db options
by
GenoMax
136k
Default `task` option is `megablast` for `blastn` which looks for `highly similar sequences` compared to `blastn` which is looking for `som…
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