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326 results • Page
2 of 7
Sort: Views
Rank
Views
Votes
Replies
1
vote
6
replies
434
views
Read multiple vcf files into R
R
vcf
26 days ago by
sousapaulo16
• 0
0
votes
4
replies
427
views
scRNA-seq quality control
qc
scrnaseq
updated 17 days ago by
jv
★ 1.2k • written 21 days ago by
sarahmanderni
▴ 100
3
votes
4
replies
424
views
Downstream analysis with DEseq2 normalization
DEseq2
integration
11 days ago by
QX
• 0
0
votes
7
replies
423
views
Using Primer3 with python to genotype a SNP at a particular position
primer3
python
position
primer
updated 15 days ago by
Pierre Lindenbaum
158k • written 15 days ago by
Keith
• 0
0
votes
2
replies
416
views
Corrupted sam file from bwa. [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped
samtools
bwa
updated 11 days ago by
jkbonfield
★ 1.2k • written 16 days ago by
tnminh89
▴ 10
1
vote
4
replies
412
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
15 days ago by
Daniel
▴ 30
3
votes
6
replies
412
views
scRNA-seq: Consistent low number of cells and low fraction reads across the samples
scRNA-seq
cells
mRNA
expression
gene
updated 6 hours ago by
jv
★ 1.2k • written 2 days ago by
newbee
▴ 40
1
vote
2
replies
412
views
Beginner needing help interpreting these articles
Machine-learning
updated 25 days ago by
Ram
41k • written 15 months ago by
Ryan
• 0
1
vote
5
replies
403
views
Spades Log not updating - ran overnight for 6 MB file, still running
Spades
Fastq
updated 24 days ago by
GenoMax
136k • written 24 days ago by
Grace
• 0
0
votes
3
replies
396
views
percentage of cells in each cluster- Seurat
seurat
updated 11 days ago by
seidel
11k • written 14 days ago by
odi
▴ 10
0
votes
4
replies
395
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
DiffBind
csaw
normalization
spikein
ChIPseq
14 days ago by
jared.andrews07
★ 16k
2
votes
4
replies
393
views
What are the steps for Germline and Somatic CNV detection using CNVkit?
cnv
cnvkit
13 days ago by
ahmad mousavi
▴ 770
4
votes
6
replies
388
views
Unexpected separation of RNA-seq samples on PCA plot
depletion
PCA
rRNA
plot
RNA-seq
11 days ago by
Tihana
▴ 10
0
votes
2
replies
382
views
trimming primers using iVar
trim
iVar
primer
updated 25 days ago by
GenoMax
136k • written 28 days ago by
binfo.sl
• 0
0
votes
1
reply
381
views
Loftee no splice site annotations
Loftee
VEP
updated 1 day ago by
AMARU
• 0 • written 21 months ago by
Filago
▴ 90
1
vote
4
replies
375
views
Efficient Bulk Data Retrieval from NCBI BioProject
ncbi
SRAtoolkit
prefetch
14 days ago by
George
• 0
0
votes
6
replies
373
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
0
votes
3
replies
372
views
Bowtie2 Error: reads file does not look like a FASTQ file
bowtie2
alignment
updated 21 days ago by
ATpoint
78k • written 12 weeks ago by
SO_Bio
• 0
4
votes
6
replies
369
views
bwa mem hangs after a few thousand reads
bwa-mem
alignment
bwa
calling
variant
2 days ago by
cee28
▴ 30
0
votes
3
replies
365
views
Two days_to_last_followups encountered when conducting Survival Analysis with TCGA Clinical Data
TCGA
Clinical
updated 13 days ago by
Zhenyu Zhang
★ 1.1k • written 25 days ago by
yukinoyou
• 0
1
vote
3
replies
361
views
Differential Gene Expression between patients and not groups
differential-gene-expression
voom
limma
updated 25 days ago by
rpolicastro
12k • written 26 days ago by
Manuel
▴ 10
1
vote
2
replies
357
views
Bulk RNAseq Salmon index building which transcriptome to use
Salmon
RNA-seq
23 days ago by
Orange
▴ 10
2
votes
5
replies
356
views
kraken2 bacteria database 250GB+
metagenomics
16s
kraken2
kraken
updated 23 days ago by
GenoMax
136k • written 23 days ago by
10mz1
• 0
0
votes
0
replies
350
views
CalcPerturbSig() Seurat
scRNA-seq
single-cell
differential-expression
Seurat
updated 11 days ago by
Ram
41k • written 9 months ago by
123
• 0
0
votes
3
replies
350
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
1
vote
6
replies
349
views
Discrepancy in total number of bases in trimmed read1 and read2 files after BBDuk
bbduk
2 days ago by
CTLong
▴ 20
0
votes
1
reply
346
views
How to use conumee segment mean for gistic input
genomics
gistic
NGS
methylation
conumee
updated 2 days ago by
sativus
▴ 10 • written 14 months ago by
Thind amarinder
▴ 340
0
votes
4
replies
346
views
Estimate Genome Size
jellyfish
genome
k-mer
23 days ago by
kirillkirilenko
▴ 20
0
votes
2
replies
345
views
encode gt of hg38 to machine learning
machine-learning
gt
updated 25 days ago by
Ram
41k • written 12 months ago by
أرْوَى
• 0
0
votes
3
replies
333
views
STAR GeneCounts for most genes are 0
STAR
RNA-seq
updated 18 days ago by
Ram
41k • written 18 days ago by
Hansel Ivander
• 0
0
votes
3
replies
333
views
ANNOVAR Error: All variants in a VCF register as "invalid genotype records in input file"
genomics
wgs
vcf
annovar
updated 9 days ago by
MatthewP
★ 1.3k • written 11 days ago by
skinny_genes
• 0
5
votes
3
replies
333
views
Strand bias in supplementary alignments from Nanopore
minimap2
nanopore
strand
updated 23 days ago by
cmdcolin
★ 3.4k • written 24 days ago by
dariober
14k
0
votes
7
replies
330
views
SNP calling with many samples using bcftools
bcftools
SNP
multithreading
15 days ago by
George
• 0
0
votes
4
replies
327
views
very few sequences classified with Kraken2
metagenomics
16s
kraken2
kraken
updated 24 days ago by
dthorbur
▴ 890 • written 25 days ago by
10mz1
• 0
4
votes
5
replies
326
views
salmon for gene expression quantification
salmon
gene-expression
updated 15 days ago by
Ram
41k • written 16 days ago by
Ashish
• 0
1
vote
5
replies
326
views
bcftools mipileup error: format error, unexpected A at line 1
bcftools
updated 18 days ago by
Jautis
▴ 520 • written 18 days ago by
jiyoung
▴ 20
0
votes
3
replies
322
views
RNA star taking more than 24h to complete 2nd pass
rna-seq
star
updated 15 days ago by
Ram
41k • written 15 days ago by
manuelmourato25
• 0
1
vote
9
replies
321
views
Htseq-count reads with missing mate encountered
htseq
htseq-count
16 days ago by
Bjorn
• 0
1
vote
2
replies
320
views
Issues with Mixture file when using CIBERSORTx
Deconvolution
CIBERSORTx
updated 13 days ago by
Hongjin
• 0 • written 8 weeks ago by
mateomejias
• 0
1
vote
3
replies
319
views
gnomAD4.0 Hail Table Downloading
NGS
gnomAD
updated 14 days ago by
Ram
41k • written 14 days ago by
adarsh_pp
▴ 30
0
votes
3
replies
318
views
Correct for different number of cells and individuals in single cell data analysis
scRNA-seq
updated 28 days ago by
Ram
41k • written 28 days ago by
Sara
▴ 230
0
votes
2
replies
318
views
How to perform liftover from 38 to 37 in R?
R
genomics
hail
liftover
gwas
13 days ago by
DN99
▴ 20
0
votes
3
replies
315
views
Package version warning - package ‘extdata’ is not available for Bioconductor version '3.17'
R
Bioconductor
updated 25 days ago by
Ram
41k • written 25 days ago by
Rob
▴ 160
0
votes
3
replies
315
views
Indexing the reference genome
STAR
updated 23 days ago by
Ram
41k • written 24 days ago by
Yasemin
• 0
2
votes
3
replies
314
views
Selecting a subset of MSigDB database for GSEA
fgsea
clusterprofiler
GSEA
14 days ago by
Orange
▴ 10
0
votes
4
replies
312
views
rpy2 package
rpy2
28 days ago by
scarlettpigany
• 0
3
votes
4
replies
310
views
Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not present in R
FDR
volcano
plotting
R
plot
updated 2 days ago by
Nitin Narwade
★ 1.5k • written 3 days ago by
RNAseqer
▴ 250
0
votes
3
replies
309
views
Annovar - Annotated file cells show string
annovar
7 days ago by
Roshan
• 0
0
votes
4
replies
308
views
Query regarding callsets used as known sites in Variant Calling
GATK
VCF
12 days ago by
Shruti Baikerikar
• 0
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 9 days ago by
TC_Chang
▴ 10
326 results • Page
2 of 7
Recent Votes
Answer: GO categorization
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
Answer: GO categorization
C: Expected a file with 2 fields per line. GenomicsDBImport from GATK ?
C: Expected a file with 2 fields per line. GenomicsDBImport from GATK ?
Answer: Problematic fastq files...How can we trust them?
Comment: Problematic fastq files...How can we trust them?
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Comment: Should I scale all genes in single cell Seurat?
by
synat.keam
▴ 80
Thanks, António for your kind and detailed responses. You helped clear my doubt about scaling! Kind Regards, Synat
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
by
Brian Bushnell
19k
It's not a silly question! And yes, it can be done. JGI is currently testing various binning tools to try to find the best protocol for t…
Answer: GO categorization
by
geneontologyhelp
▴ 270
[We have this in our FAQ][1]. PANTHER version 18.0, which powers the enrichment analysis on our homepage, has [143 species][2] loaded and …
Comment: Problematic fastq files...How can we trust them?
by
blackadder
▴ 30
Thanks for the feedback fellas! I agree with the aforementioned!
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.
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