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702 results • Page
4 of 15
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Views
Votes
Replies
1
vote
2
replies
243
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
5 days ago by
bioinfo
▴ 150
0
votes
3
replies
278
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 6 days ago by
noodle
▴ 580 • written 7 days ago by
doramora
▴ 10
0
votes
1
reply
152
views
Post-imputation QC for input into GWAS analyses
gwas
prs
updated 6 days ago by
LauferVA
4.2k • written 7 days ago by
graeme.thorn
▴ 100
0
votes
2
replies
210
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
6 days ago by
melissa.joubert
• 0
4
votes
1
reply
218
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
7 days ago by
J.
▴ 40
0
votes
0
replies
117
views
Is there a real ground truth for CNV data?
CNV
7 days ago by
jennyp0706
• 0
0
votes
3
replies
226
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 7 days ago by
GenoMax
142k • written 7 days ago by
RNAseqer
▴ 270
1
vote
1
reply
152
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 6 days ago by
Ram
44k • written 7 days ago by
kilcdincer
▴ 10
4
votes
4
replies
3.0k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 7 days ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
1
vote
8
replies
484
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
updated 3 days ago by
Alex Reynolds
35k • written 7 days ago by
ntsopoul
▴ 60
0
votes
3
replies
219
views
How to access GWAVA software of data
GWAVA
updated 7 days ago by
GenoMax
142k • written 7 days ago by
nonaddldy
▴ 10
0
votes
2
replies
234
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
5 days ago by
Chen
• 0
1
vote
1
reply
182
views
The total expressed genes in RNA-Seq data
RNA-SEQ
updated 7 days ago by
ATpoint
82k • written 7 days ago by
Pegasus
▴ 100
0
votes
1
reply
137
views
What is the bin size for Bamcompare?
chip-seq
deeptools
bamcompare
updated 6 days ago by
Ram
44k • written 7 days ago by
Emily
▴ 20
1
vote
3
replies
293
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 4 days ago by
GenoMax
142k • written 7 days ago by
ohtang7
▴ 40
0
votes
0
replies
98
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
7 days ago by
Spring
• 0
0
votes
2
replies
196
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
7 days ago by
IdaHao0921
• 0
0
votes
3
replies
362
views
Snakemake wrapper issue
fastqc
snakemake
updated 7 days ago by
Wei-Chen Pan
• 0 • written 10 weeks ago by
Matvii Mykhailichenko
• 0
2
votes
5
replies
292
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 7 days ago by
Philipp Bayer
8.5k • written 7 days ago by
林明德
• 0
0
votes
4
replies
2.3k
views
MGLTools does not work in windows 11
windows-11
Autodock
windows
MGLTools
updated 6 days ago by
Ram
44k • written 13 months ago by
mohyeddine.taleb
• 0
2
votes
4
replies
242
views
Help with IGV abbreviation
igv
updated 6 days ago by
Ram
44k • written 7 days ago by
GeneC
• 0
0
votes
1
reply
168
views
How to process Bulk WES data?
WES
WGS
updated 7 days ago by
GenoMax
142k • written 7 days ago by
wyuan37
• 0
0
votes
1
reply
165
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 7 days ago by
GenoMax
142k • written 7 days ago by
cedric.blais
• 0
0
votes
2
replies
444
views
News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
7 days ago by
David Langenberger
11k
0
votes
1
reply
155
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 7 days ago by
Ram
44k • written 7 days ago by
eking28
• 0
2
votes
5
replies
523
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 6 days ago by
Ram
44k • written 12 days ago by
Prawesh
• 0
1
vote
3
replies
457
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
7 days ago by
kalavattam
▴ 190
1
vote
2
replies
275
views
How to interpret infinite odds ratio?
statistics
7 days ago by
Lukas
• 0
4
votes
2
replies
199
views
Duplicated sequence samtools
bowtie2
samtools
updated 7 days ago by
GenoMax
142k • written 8 days ago by
Moinuddin
• 0
0
votes
0
replies
108
views
reference-free assembly error assessment tools
assembly
8 days ago by
lagartija
▴ 160
2
votes
4
replies
314
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
6 days ago by
Esraa
• 0
2
votes
0
replies
151
views
Herald:
The Biostar Herald for Monday, May 13, 2024
herald
8 days ago by
Biostar
2.8k
0
votes
1
reply
148
views
Splitting Seurat object by sample layers
seurat
updated 7 days ago by
Ram
44k • written 8 days ago by
kilcdincer
▴ 10
0
votes
4
replies
273
views
Galaxy StringTie error
stringtie
galaxy
7 days ago by
trkfs
• 0
0
votes
0
replies
107
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
8 days ago by
atariw
▴ 10
0
votes
1
reply
164
views
Mouse ribosome sequences in fasta format
fasta
mm10
rRNA
updated 8 days ago by
GenoMax
142k • written 8 days ago by
octpus616
▴ 100
1
vote
4
replies
362
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 6 days ago by
Juke34
8.6k • written 8 days ago by
Vijith
▴ 30
0
votes
1
reply
168
views
consensus sequence calling
consensus
updated 8 days ago by
bk11
★ 2.5k • written 8 days ago by
Ghada
• 0
0
votes
3
replies
204
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat
single-cell
scRNA-seq
R
updated 7 days ago by
Ram
44k • written 8 days ago by
yau
• 0
3
votes
2
replies
290
views
imputation through beagle
panel
beagle
reference
imputation
7 days ago by
analyst
▴ 50
0
votes
0
replies
92
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
8 days ago by
JACKY
▴ 140
0
votes
1
reply
550
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
updated 8 days ago by
aw7
▴ 300 • written 4 weeks ago by
abhishekghadge
• 0
3
votes
1
reply
230
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
updated 8 days ago by
aw7
▴ 300 • written 12 days ago by
Zeng Hao
▴ 40
0
votes
0
replies
107
views
Reference panel of normals for ensembl named refgenome
Mutect2
8 days ago by
gernophil
▴ 80
1
vote
0
replies
101
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
8 days ago by
tomas4482
▴ 400
2
votes
6
replies
415
views
BWA alignment
Samtools
bam
updated 6 days ago by
a.alnawfal.1992
▴ 260 • written 8 days ago by
Vahid
• 0
3
votes
2
replies
207
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 8 days ago by
ATpoint
82k • written 8 days ago by
jennyp0706
• 0
0
votes
1
reply
164
views
Manual Assembly and Protein Translation, HELP, assignment revision
sequence
university
assembly
protein
genomics
updated 8 days ago by
Philipp Bayer
8.5k • written 9 days ago by
samRayne
• 0
0
votes
1
reply
254
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Mendelian-Randomization
updated 7 days ago by
Ram
44k • written 11 days ago by
Nikki
• 0
2
votes
14
replies
3.0k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 7 days ago by
Anitha
• 0 • written 4.9 years ago by
ww22runner
▴ 60
702 results • Page
4 of 15
Recent Votes
Answer: tensorQTL interaction issue
Answer: converting transcript IDs (Ensembl) to gene symbols in R
Answer: converting transcript IDs (Ensembl) to gene symbols in R
Comment: Trimming tool
Answer: Trimming tool
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
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Comment: Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis o
by
Shukai
• 0
Thank you Ram for the comments! Noted for future posts.
Comment: Where to find old version of GATK best practice
by
Zhenyu Zhang
★ 1.2k
I am looking for diagrams, and step-by-step instructions of how to build my pipelines. I think the github is only helpful if you are a wdl…
Comment: Where to find old version of GATK best practice
by
Zhenyu Zhang
★ 1.2k
oh, this is helpful. Thanks.
Comment: Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis o
by
Ram
44k
1. You can edit your post and add relevant details. There is no need to add separate comments with relevant details especially when it's no…
Answer: Functional enrichment analysis for unique gene IDs
by
geneontologyhelp
▴ 400
If you are looking at producing GO annotations, we currently only recommend InterProScan, and basically only for novel organisms or where t…
Answer: Question about samtools view flags (paired reads vs. properly paired reads)
by
Pierre Lindenbaum
161k
paired reads = the experiment was a paired end assay: each fragment was sequenced on 5' and 3', two FASTQ files are generated by the seque…
Answer: z-score of gene set
by
Matthias Zepper
4.6k
The z-score is a measure of how many standard deviations a particular data point is from the mean of a distribution. A positive z-score ind…
Answer: converting transcript IDs (Ensembl) to gene symbols in R
by
bk11
★ 2.5k
You can do as following: library(biomaRt) # Set up the Ensembl BioMart connection ensembl <- useEnsembl(biomart = "genes",…
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w
by
Pierre Lindenbaum
161k
well you try to use FastaAlternateReferenceMaker https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMak…
Comment: z-score of gene set
by
bk11
★ 2.5k
Can you please tell us what will be your propose of z-score calculation?
Comment: DRAGEN gVCF files and joint calling GATK-GenomicsDB
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DBScan
▴ 300
I think I did it once, but why would you use GATK with DRAGEN gVCF files? If you have a DRAGEN, the iterative gVCF Genotyper does a much fa…
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beantkapoor16
▴ 10
So, I just tested it and it's performing much better now. Most of the haplotype paths are coming from the expected haplotypes (australasica…
Comment: Kraken2 Custom Database non-deterministic results
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Thank you!
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161k
there is not enough information. you have to show us the command you used, a snapshot of your fasta...
Comment: Practical Haplotype Graph v2 not finding correct paths
by
beantkapoor16
▴ 10
That's great. I will test it and let you know how it goes. Thank you.
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