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328 results • Page
2 of 7
Sort: Rank
Rank
Views
Votes
Replies
1
vote
4
replies
270
views
Bowtie mapping for single_end read
bowtie
3 days ago by
Rita
• 0
0
votes
0
replies
107
views
missing region in the process of annotation
annotatr
minfi
3 days ago by
Aki
▴ 10
1
vote
0
replies
99
views
Visualize and explore eventalign data against reference
igv
minimap
nanopolish
nanopore
ngs
3 days ago by
joe
▴ 390
0
votes
6
replies
372
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
RNA-Seq
Nanopore
ONT
differential
expression
2 days ago by
tw_140
• 0
9
votes
15
replies
780
views
Construction of single sequence assembly out of contigs
Contigs
Bacteria
Genome
WGS
2 days ago by
analyst
▴ 10
0
votes
0
replies
98
views
Differentiate sequenced and imputed variants in BGEN files
imputation
bgen
ukb
4 days ago by
user230613
▴ 350
0
votes
4
replies
271
views
Species coverage in the NCBI protein NR database ?
NR
updated 4 days ago by
Istvan Albert
99k • written 4 days ago by
HERMAN
▴ 10
0
votes
0
replies
105
views
addPatternDensity to qsea object
maxDensityPattern
medip
qsea
4 days ago by
Jaykishan
• 0
1
vote
1
reply
168
views
Harmony integration PC variance explained
scRNA
integration
harmony
updated 2 days ago by
CTLong
▴ 20 • written 4 days ago by
e.iich
• 0
0
votes
3
replies
236
views
merged rs number information
merged
dbsnp
3 days ago by
sskimvd
• 0
1
vote
1
reply
167
views
Beginner differential methylation analysis
Methylation
updated 4 days ago by
Basti
★ 1.9k • written 4 days ago by
a.basitkhan1990
▴ 30
2
votes
1
reply
241
views
EnhancedVolcano underrepresenting DEGs
R
updated 3 days ago by
Kevin Blighe
86k • written 5 days ago by
jabbari.parnian
▴ 30
0
votes
0
replies
113
views
[maftools]Too many multi_hit and missense mutation
maftools
gatk
MAF
data
WES
VCF
5 days ago by
jiazheng_lin
• 0
0
votes
0
replies
125
views
Negative F statistics for sex check in plink
plink
check
sex
5 days ago by
kl
▴ 10
0
votes
1
reply
195
views
Chipseq peak calling and peak frequency region
chipseeker
macs2
updated 3 days ago by
Arup Ghosh
3.2k • written 5 days ago by
Mehwish
▴ 10
0
votes
1
reply
252
views
issue in RNA -seq analysis
NGS
RNA-Seq
updated 6 days ago by
GenoMax
136k • written 6 days ago by
subhiksha
• 0
0
votes
3
replies
348
views
Alternatives to Music2 for rnaseq deconvolution without disease scRNA dataset
scRNA
deconvolution
Music
Music2
bulk
updated 6 days ago by
ATpoint
78k • written 7 days ago by
manuelmourato25
• 0
0
votes
3
replies
306
views
Annovar - Annotated file cells show string
annovar
7 days ago by
Roshan
• 0
0
votes
1
reply
246
views
MinKNOW software installation doubt for MinION Nanopore sequencing
MinKNOW
MinION
Nanopore
updated 6 days ago by
GenoMax
136k • written 7 days ago by
Soumajit
▴ 40
0
votes
1
reply
218
views
htShinyExample-5.3 - not working
htShiny
Oncoprint
InteractiveComplexHeatmap
updated 1 day ago by
Ram
41k • written 7 days ago by
bioinfo
▴ 60
0
votes
0
replies
159
views
Seeking Advice on WGCNA for Nematode Sexual Dimorphism
WGCNA
Worms
RNA-Seq
7 days ago by
kdca
• 0
0
votes
3
replies
275
views
labelling the clusters from the CD4 T cell scRNAseq data
scRNAseq
7 days ago by
Sara
▴ 230
0
votes
0
replies
881
views
Any tools for finding the telomere sequences / lengths directly for nanopore sequencing reads without any prior knowledge of the organism
genomics
telomeres
reads
7 days ago by
Mark
• 0
0
votes
0
replies
156
views
not best k value found
de
assemblly
assembly
novo
kmergenie
7 days ago by
shaileshdesai76
• 0
0
votes
0
replies
166
views
Multi-mapped reads in Ribo-Seq data, discard or keep?
STAR
ribo-seq
multi-mapped
rna-seq
TE
7 days ago by
Carmen
• 0
0
votes
0
replies
170
views
Identifying differentially expressed loci for gene duplicates using DESeq2
rna-seq
deseq2
8 days ago by
pl23
• 0
0
votes
2
replies
289
views
Find Genes in Homer Analysis that have the enriched Motif
single
ORA
nucleus
mRNA
Homer
3 days ago by
je71xusa
• 0
0
votes
2
replies
277
views
Tool to get genes in the neighbourhood of a particular gene
locus
Gene
updated 8 days ago by
Raony Guimarães
★ 1.3k • written 8 days ago by
ThePlaintiff
▴ 80
2
votes
9
replies
665
views
Salmon (or other pseudo-mappers) for multi-species RNAseq read filtering
STAR
Salmon
mapper
aligner
RNAseq
1 day ago by
ian.will
▴ 10
5
votes
2
replies
248
views
RNA Contamination Tool for Developing Cell Samples
contamination
scRNA
quality
RNA
SoupX
7 days ago by
Rafael Soler
★ 1.2k
1
vote
2
replies
200
views
DOES MGI SEQUENCING RESULT CONTAINS MULTIPLE FILES FOR SINGLE SAMPLE
whole
genome
assembly
sequencing
updated 8 days ago by
WouterDeCoster
47k • written 8 days ago by
manaswiniparija3
▴ 10
1
vote
0
replies
140
views
What are the methods to correlate/study metabolomics data to proteomics data?
metabolomics
proteomics
multiomics
8 days ago by
WUSCHEL
▴ 720
0
votes
3
replies
305
views
R ComplexHeatmap - Dividing Column Annotation into Distinct Y-Axis Scales
R
complexheatmap
updated 3 days ago by
jv
★ 1.2k • written 8 days ago by
TC_Chang
▴ 10
0
votes
0
replies
113
views
Find equivalent pathways between KEGG, Reactome, and WikiPathways
pathway
mapping
database
8 days ago by
Ngrin
• 0
0
votes
0
replies
126
views
GenAlEx Haploid Data Detecting Recombination
GenAlEx
Popgen
Haploid
Recombination
8 days ago by
turcoa1
• 0
0
votes
0
replies
130
views
TF Footprinting using HINT ATAC module from RGT
hintatac
footprinting
rgttoolbox
atacseq
9 days ago by
alphaflylizard
• 0
0
votes
2
replies
264
views
Creating a Variant containing FASTA for proteomics search from VCF and genomic FASTA
translation
Variant
proteomics
FASTA
VCF
8 days ago by
chscho
• 0
0
votes
0
replies
118
views
Trouble making a ggmsa alignment plot
R
ggmsa
9 days ago by
andre.arrudalima
▴ 30
0
votes
0
replies
112
views
cNMF vs LIGER
NMF
correction
batch
9 days ago by
e.r.zakiev
▴ 170
1
vote
4
replies
303
views
Analyze with Geo2R
R
NCBI
7 days ago by
anasjamshed
▴ 120
0
votes
0
replies
869
views
For people doing high molecular weight DNA sequencing library prep, do you see a steep drop off in the fragment sizes before and after the library pr…
library-prep
sequencing
ont
nanopore
ngs
9 days ago by
Mark
• 0
0
votes
0
replies
130
views
Creating heatmap for ChIP-seq using deeptools
heatmap
chipseq
chip
deeptools
visualization
9 days ago by
biology_inform
▴ 50
0
votes
1
reply
138
views
error in plink
polygenicriskscore
prscalculation
prs
plink
error
updated 9 days ago by
biofalconch
★ 1.1k • written 9 days ago by
Emilija
• 0
0
votes
2
replies
213
views
how to use pilon
genome
pipelines
assembly
pilon
contig
updated 3 days ago by
Arup Ghosh
3.2k • written 9 days ago by
vasudhapai
• 0
3
votes
2
replies
242
views
t-test by row
R
t-test
updated 9 days ago by
dthorbur
▴ 890 • written 9 days ago by
sooni
▴ 10
0
votes
0
replies
110
views
jellyfish histo is empty
jellyfish
kmer
fastq
9 days ago by
m.t.lorenc
• 0
0
votes
0
replies
124
views
Retrieving NM:i edit distance field in .sam files generated by vg giraffe and vg surject
giraffe
surject
vg
9 days ago by
cassiwatt
• 0
1
vote
2
replies
210
views
How to identify the nearest gene associated with a specific SNPs?
RSID
GWAS
updated 10 days ago by
Jeremy
▴ 850 • written 10 days ago by
camillab.
▴ 150
0
votes
1
reply
169
views
WGCNA convenience function
WGCNA
updated 9 days ago by
andres.firrincieli
3.5k • written 10 days ago by
fluentin44
• 0
0
votes
0
replies
121
views
Low mapping after Cufflinks assembly
assembly
gffread
cuffmerge
Cufflinks
RSEM
10 days ago by
sofiablancoglez
• 0
328 results • Page
2 of 7
Recent Votes
Comment: Problematic fastq files...How can we trust them?
Comment: Problematic fastq files...How can we trust them?
Comment: Merging FASTQ files with Cellranger
Finding human .vcf files online to download
Answer: Should I scale all genes in single cell Seurat?
Answer: Should I scale all genes in single cell Seurat?
Answer: Should I scale all genes in single cell Seurat?
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Gama313
▴ 120
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▴ 30
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Recent Replies
Comment: Which program, tool, or strategy do you use to visualize genomic rearrangements?
by
cmdcolin
★ 3.4k
i collect a large list of tools for visualization, some are specialized for SVs and re-arrangements. you can filter by tag (SV, CNV, compar…
Answer: The number of variations in the pan-genome is reduced compared to the variations
by
Jordan M Eizenga
▴ 410
If variants overlap in the genome, `vg deconstruct` will combine them into one locus with multiple alleles. If your input VCF has a lot of …
Answer: How to find node Postion and source(sample) ?
by
Jordan M Eizenga
▴ 410
You can use `vg find -P` for this. This command is not really designed to be used frequently throughout the genome (each invocation loads t…
Comment: How Can I move the scattered dots more closer into the center of box ?
by
Brian Bushnell
19k
I would just draw them in by hand where you want them.
Comment: How to identify CG, CHG, or CHH from MeDIP data
by
Tm
★ 1.1k
I know that CpG types can be identified using whole genome bisulphite data. But could it be possible using MeDIP data too? We tried using Q…
Comment: Problematic fastq files...How can we trust them?
by
Brian Bushnell
19k
I'd have to agree there... while you can generally recover a fastq to the point that it is spec-compliant, you don't know how or why the f…
Answer: Finding human .vcf files online to download
by
cmdcolin
★ 3.4k
---------- some common ones include 1000 genomes vcf (large, multi-sample) http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ …
Comment: GO categorization
by
m.habib
• 0
Thanks Istvan for your reply. I think these programs will do the same as Trinotate. Trinotate searches against numerous databases and gener…
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
by
jv
★ 1.2k
I wonder if using cell hashing, which would allow pooling of cells from multiple samples before droplet formation, could improve things her…
Comment: Where Can I Find The Basepair Positions Of Chromosome Bands?
by
Malachi Griffith
19k
And the hg38 version can be found here: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/cytoBand.txt.gz And for convenience, upda…
Answer: How Can I move the scattered dots more closer into the center of box ?
by
Trivas
★ 1.5k
You added a position dodge on your boxplot but not on your points.
Comment: How Can I move the scattered dots more closer into the center of box ?
by
ATpoint
78k
Please understand that biostars is not a helpdesk for trivial ggplot questions. Google it and find help on previous StackExchange sites, or…
Comment: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates with
by
jucosie
• 0
Hello, I am reviewing some old scripts in which I used clumpify.sh (BBMap 38.90) with the following parameters: ./clumpify.sh in1=$d…
Comment: Problematic fastq files...How can we trust them?
by
Istvan Albert
99k
perhaps ask her about the origin of the data, how was the data postprocessed FASTQ data is a bit more resilient than other types of data a…
Answer: GO categorization
by
Istvan Albert
99k
If you have an organism that lacks the GO to gene mapping then you have to find a way to assign these terms to your genes. Basically your …
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