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1,000 results • Page
6 of 20
Sort: Rank
Rank
Views
Votes
Replies
1
vote
0
replies
153
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
updated 9 days ago by
zx8754
11k • written 12 days ago by
Emilie
▴ 10
0
votes
0
replies
142
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
12 days ago by
Javier
• 0
0
votes
2
replies
292
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 2 days ago by
Zhenyu Zhang
★ 1.2k • written 12 days ago by
yahn
• 0
0
votes
0
replies
134
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic
Variant
predisposition
12 days ago by
mikemakaveli1
• 0
2
votes
2
replies
238
views
Raw counts using stringtie
stringtie
RNA-seq
updated 12 days ago by
GenoMax
142k • written 12 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
134
views
Modify plot R mtDNA indel
plot
mtDNA
R
12 days ago by
marco.barr
▴ 110
0
votes
0
replies
329
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
12 days ago by
NorbertK
▴ 10
4
votes
2
replies
257
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 10 days ago by
Ram
43k • written 12 days ago by
carolofharvest
▴ 40
13
votes
14
replies
889
views
High Malat-1 expression in single cell data
single-cell
updated 7 days ago by
t.montserrat.ayuso
▴ 40 • written 16 days ago by
carolofharvest
▴ 40
0
votes
2
replies
277
views
Downloading older version of a tool
Alignment
tools
11 days ago by
Ruqaiya
• 0
0
votes
0
replies
154
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
12 days ago by
rustykb
▴ 20
1
vote
1
reply
201
views
DSEQ2 analysis
DESEQ2
logfoldchange
updated 10 days ago by
Ram
43k • written 12 days ago by
adi.gershon1
• 0
3
votes
5
replies
326
views
Generating mpileup file using samtools
mpileup
samtools
updated 12 days ago by
Joe
21k • written 12 days ago by
Ruqaiya
• 0
0
votes
5
replies
404
views
6 follow
What purposes can TPM values be used for?
RNA-seq
TPM
Normalization
DESeq2
updated 12 days ago by
b.contreras.moreira
▴ 180 • written 13 days ago by
JH
• 0
1
vote
3
replies
303
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ
RNAseq
updated 12 days ago by
ATpoint
82k • written 12 days ago by
Qi
• 0
0
votes
0
replies
144
views
News:
Cellosaurus release 49 is available
cell
biocuration
line
database
news
knowledgebase
12 days ago by
Amos Bairoch
▴ 120
2
votes
3
replies
319
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 12 days ago by
dthorbur
★ 2.0k • written 12 days ago by
Vijith
▴ 30
0
votes
0
replies
159
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
12 days ago by
Jeyong
• 0
0
votes
2
replies
741
views
homer not configured properly
Homer
makeTagDirectory
updated 12 days ago by
clairechung112
• 0 • written 24 months ago by
amahdi779
• 0
1
vote
3
replies
301
views
Bedtools merge minimum overlap?
bedtools
genomics
updated 12 days ago by
Alex Reynolds
35k • written 12 days ago by
SJP
• 0
0
votes
0
replies
145
views
Empty table plot using plotGseaTable()
FGSEA
11 days ago by
Chris
▴ 280
0
votes
1
reply
205
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
updated 12 days ago by
anovak
▴ 120 • written 13 days ago by
Hang
• 0
1
vote
3
replies
260
views
DiffBind: no peaks in DBA
MACS2
DiffBind
ChIP-seq
updated 12 days ago by
jared.andrews07
★ 16k • written 13 days ago by
yvonneh
▴ 10
3
votes
5
replies
374
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
12 days ago by
Maverick
▴ 10
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 12 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
225
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
12 days ago by
dtnondorf
• 0
3
votes
8
replies
674
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
updated 8 days ago by
Chris Dean
▴ 410 • written 13 days ago by
sovrappensiero
▴ 100
1
vote
2
replies
267
views
RNA-seq data for deep learning classification
rna-seq
12 days ago by
yahn
• 0
3
votes
8
replies
568
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
8 days ago by
Qroid
▴ 40
0
votes
1
reply
531
views
Loss of 'var' using concatenation of AnnData objects
Scanpy
AnnData
updated 13 days ago by
Hugo
• 0 • written 5 months ago by
Rachel
• 0
0
votes
1
reply
173
views
Provean help
variant
Provean
updated 12 days ago by
Mensur Dlakic
★ 27k • written 13 days ago by
Arun Sai Kumar
• 0
1
vote
1
reply
179
views
Download eQTL data of one specific gene for all tissues from GTEx
eQTL
GTEx
updated 13 days ago by
bk11
★ 2.4k • written 13 days ago by
Jeol
▴ 20
1
vote
1
reply
187
views
Super ehancers
enhancers
updated 13 days ago by
jared.andrews07
★ 16k • written 13 days ago by
Oburah
• 0
4
votes
7
replies
389
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
1 day ago by
Chen
• 0
5
votes
5
replies
309
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA
DADA2
metabarcoding
updated 13 days ago by
atharvakarkare14
▴ 30 • written 13 days ago by
Begonia_pavonina
▴ 150
1
vote
7
replies
482
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
12 days ago by
eebloom
▴ 80
3
votes
3
replies
358
views
What analysis suitable to identify similarly expressed genes between two samples (treated vs untreated). Contrary to DGE analysis,
Gene-Expression
RNA
NOISeq
DGE
updated 12 days ago by
ATpoint
82k • written 13 days ago by
alifafiq1
• 0
0
votes
0
replies
104
views
Use of annotation of integrated Seurat object in single sample
Seurat
13 days ago by
Bine
▴ 60
0
votes
0
replies
114
views
News:
Beyond beginner R: Advancing your coding skills - September 16-19
Advanced-Coding
Programming
R
updated 13 days ago by
Ram
43k • written 13 days ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
249
views
Subsetting and merging back Seurat Object brings different results
Seurat
13 days ago by
Bine
▴ 60
0
votes
0
replies
171
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
NGS
Genomics
Post-doc
R-loops
updated 13 days ago by
Ram
43k • written 13 days ago by
4r-rtg
• 0
1
vote
1
reply
156
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 13 days ago by
Ram
43k • written 13 days ago by
marco.barr
▴ 110
0
votes
0
replies
105
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
13 days ago by
Vijith
▴ 30
10
votes
14
replies
732
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 8 days ago by
GenoMax
142k • written 14 days ago by
nicole.kavanagh
• 0
0
votes
1
reply
292
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
updated 13 days ago by
Scooter
▴ 280 • written 20 days ago by
avocado123
• 0
0
votes
0
replies
109
views
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
13 days ago by
James
▴ 10
0
votes
1
reply
600
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 13 days ago by
mdav
• 0 • written 19 months ago by
Zoe
• 0
1
vote
3
replies
276
views
Odd alignment question/finding
Alignment
updated 12 days ago by
barslmn
★ 2.1k • written 13 days ago by
poordumbsillyidiot
• 0
0
votes
1
reply
222
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 13 days ago by
GenoMax
142k • written 13 days ago by
mgranada3
▴ 30
0
votes
0
replies
132
views
Looking for the best way to interpret these data
RNA-seq
ontology
GO
updated 13 days ago by
Ram
43k • written 13 days ago by
Oscar
▴ 10
1,000 results • Page
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Recent Votes
Answer: Genotyping sites with N in reference genome
A: how to combine RNA seq data from 4 lanes
Answer: Cannot install bwa-mem2 via conda
Answer: Sub-sampling a BAM to a fixed number of reads
Comment: Downsample BAM file to specific amount of reads
Answer: Long reads and fixing of mate-pair issues/marking duplicates with samtools
Answer: Long reads and fixing of mate-pair issues/marking duplicates with samtools
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Recent Replies
Comment: Genotyping sites with N in reference genome
by
Zhenyu Zhang
★ 1.2k
Whether N -> A/T/G/C represents a variant is heavily dependent on the tool itself, and I know most tools don't. Since you don't see it in y…
Comment: calculating genomic coverage/ base overlap in R
by
marco.barr
▴ 110
The code seems correct at first glance... How did you generate the data in the Excel file? Have you checked the exon annotations? You could…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Did you remeber to unzip/untar the `nt` preformatted files that you downloaded?
Comment: Genotyping sites with N in reference genome
by
shpak.max
▴ 50
Just to clarify, I have set additional sites in the reference genome to 'N', which means (based on your statement) that these will not be g…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
Pierre Lindenbaum
161k
see https://www.biostars.org/p/9496674/ <!-- when i runed blastn(version 2.15) and nt database(latest version). I used aspera to download…
Answer: Genotyping sites with N in reference genome
by
Pierre Lindenbaum
161k
> Does UnifiedGenotyper skip/ignore sites where the reference genotype is N yes. The variant is in YOUR data, not in the reference where '…
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline?
by
yura.grabovska
▴ 70
Do you have samples that should in theory have a good degree over overlap in terms of cell types across the two sequencing types? I would …
Comment: Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
by
asalimih
▴ 60
I found out that vep is only checking the GT field therefore assigning HOM to the Zygosity. Therefore the problem should be from deepvarian…
Comment: Add stats to boxplot in R
by
Lélé
• 0
To remove "Kruskall Wallis" you can try adding the argument label="p" or label = "p.signif" which displays the p-value or *** like this: …
Answer: Sequencing Depth (Read Depth) Calculations
by
GenoMax
142k
You could also use `pandepth` ([**LINK**][1]) or `mosdepth` ([**LINK**][2]) as well. These will allow you to be flexible about windowed cov…
Comment: Sequencing Depth (Read Depth) Calculations
by
Pierre Lindenbaum
161k
it looks looks ok to me. <!-- This cmd works and gives me 40.5235, I was wondering whether this cmd is right or wrong, and does anyone hav…
Comment: Add stats to boxplot in R
by
Ghada
• 0
Great. thats work. Do you know how can I remove the kruskall-Wallis name from the plot? Also I would like to draw a line under the kruskall…
Comment: Using ggplotly in R
by
jared.andrews07
★ 16k
Again, this is not particularly difficult to do with [plotly itself](https://plotly.com/r/line-and-scatter/#adding-color-and-size-mapping) …
Comment: Duplicated reads (IDs) from nanopore sequencing
by
GenoMax
142k
If you only have supplementary alignments then they may be caused by reasons mentioned here --> https://www.biostars.org/p/308853/ I did no…
Comment: Cannot install bwa-mem2 via conda
by
Pierre Lindenbaum
161k
> Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the c…
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