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Limit : this week
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224 results • Page
3 of 5
Sort: replies
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Votes
Replies
0
votes
3
replies
1.3k
views
how to calculate BAF and LRR from VCF or BCF files?
SNP
BAF
LRR
Variation
5 days ago by
xiaoguang
▴ 130
1
vote
3
replies
275
views
Question regarding MACS2 approach of peak calling
MACS2
sequencing-depth
chipseq
updated 6 days ago by
ATpoint
76k • written 14 days ago by
rkc5
• 0
3
votes
3
replies
354
views
Forum:
Importance of Data Structures for Bioinformatics?
data-structures
updated 4 days ago by
Ram
40k • written 5 days ago by
S
• 0
0
votes
3
replies
496
views
CNV calling
CNV
NGS
Variant-Calling
updated 6 days ago by
Zhenyu Zhang
▴ 980 • written 8 months ago by
adarsh_pp
▴ 30
1
vote
3
replies
312
views
I have performed Trimmomatic run for adapter removal. QC report shows drop in the reads and presence of overrepresented sequences. Seeking help!
NGS
bioinformatics
illumina
WGS
updated 16 hours ago by
swbarnes2
13k • written 1 day ago by
Vijith
▴ 30
2
votes
3
replies
1.5k
views
Racon command line with paired-ends Illumina reads
Illumina
Racon
updated 4 days ago by
Ram
40k • written 2.1 years ago by
A_heath
▴ 140
0
votes
3
replies
853
views
Mapping fastq files to reference genome
reference-genome
mapping
fastq
updated 4 days ago by
Ram
40k • written 2.3 years ago by
A_heath
▴ 140
1
vote
3
replies
328
views
VDJ reconstitution from 3' 10x genomics platforms
VDJ
updated 6 days ago by
Ram
40k • written 7 days ago by
gal.dadi
• 0
1
vote
3
replies
222
views
Finding sequences in unannotated genomes using reference coordinates
consensus
VCF
updated 3 days ago by
Ram
40k • written 3 days ago by
Prangan
▴ 20
4
votes
3
replies
989
views
INSTALLING DEseq2 via conda
DEseq2
conda
RNA-seq
updated 6 days ago by
Ram
40k • written 4 months ago by
Fizzah
▴ 30
0
votes
3
replies
727
views
How to add translation of CDS in Artemis?
translation
Artemis
updated 4 days ago by
Ram
40k • written 2.7 years ago by
A_heath
▴ 140
1
vote
3
replies
259
views
How to find out what adapters to remove after FastQC of RNAseq data?
Trimmomatic
FastQC
NGS
RNA-seq
22 hours ago by
ella
• 0
0
votes
3
replies
252
views
Errors while trying to run Scenic
Scenic
updated 6 days ago by
GenoMax
134k • written 6 days ago by
Stavroula
• 0
2
votes
3
replies
600
views
How to change standard genetic code in Artemis?
Mycosplasma
Artemis
updated 4 days ago by
Ram
40k • written 2.8 years ago by
A_heath
▴ 140
1
vote
3
replies
672
views
How to determine plasmid or chromosomal origin?
plasmid
chromosomal-origin
updated 4 days ago by
Ram
40k • written 3.0 years ago by
A_heath
▴ 140
0
votes
3
replies
250
views
how to extract unique snps in a vcf file by comparing with multiple vcf files
bcftools
SNP
GATK
VCF
updated 1 day ago by
Pierre Lindenbaum
157k • written 4 weeks ago by
nikhil
▴ 20
0
votes
3
replies
265
views
How to find target genes From RNA seq data?
Cotton
DGE
RNA-seq
updated 6 days ago by
Ram
40k • written 6 days ago by
Fizzah
▴ 30
1
vote
3
replies
351
views
How to DESeq2 using miRNA data obtained using TCGAbiolinks
R
TCGAbiolinks
DESeq2
TCGA
updated 3 days ago by
Zhenyu Zhang
▴ 980 • written 5 days ago by
Mo
• 0
2
votes
3
replies
278
views
Can I infer the fraction of replicating cells from bulk RNA-seq data?
replication
apoptosis
updated 5 days ago by
Ram
40k • written 5 days ago by
txema.heredia
▴ 80
1
vote
3
replies
239
views
Sub-sampleing bam files based on sequencing_summary.txt (guppy output)
samtools
guppy
updated 5 days ago by
GenoMax
134k • written 5 days ago by
anika.john
• 0
1
vote
3
replies
274
views
Fastqc loop
fastQC
r
RNA-seq
6 days ago by
camillab.
▴ 130
0
votes
2
replies
906
views
STAR-FUSION error
STAR-FUSION
CTAT
updated 12 hours ago by
Ram
40k • written 14 months ago by
mc123
• 0
0
votes
2
replies
565
views
News:
The Practice of RADseq: Population Genomics Analysis with Stacks (RADS02) Early bird deadline approaching - 20th September
population-genomics
radseq
stacks
updated 6 days ago by
Dave Carlson
★ 1.4k • written 7 days ago by
oliverhooker
▴ 110
1
vote
2
replies
219
views
STAR error EXITING because of FATAL ERROR: failed reading from temporary file
STAR
RNA-seq
updated 6 days ago by
GenoMax
134k • written 6 days ago by
erik.burchard
▴ 20
0
votes
2
replies
332
views
Extract Divergence Times and Corresponding Node Numbers from a Time Tree
phylogeny
R
ape
phytools
phylogenetics
6 days ago by
Simone
• 0
0
votes
2
replies
556
views
module and trait correlation for WGCNA
treatment
WGCNA
relation
microarray
module-treatment
updated 6 days ago by
AS-git
• 0 • written 6 months ago by
Shriyansh
• 0
2
votes
2
replies
207
views
Kraken2 recovering only classified reads
Kraken2
taxonomy
classification
5 days ago by
SushiRoll
▴ 110
4
votes
2
replies
422
views
Recommended way to normalize SmartSeq2 gene expression matrix to better match 10X expression data
rna-seq
smartseq2
r
updated 5 days ago by
yhdist
▴ 70 • written 8 days ago by
Cookin
▴ 10
3
votes
2
replies
469
views
Conflict between MAFFT and new PRANK installation
multiple-sequence-alignment
bash
prank
mafft
phylogenetics
updated 5 days ago by
Ram
40k • written 19 months ago by
noramarie
• 0
0
votes
2
replies
232
views
Is it okay to just average the log2FC values across different cell types in pseudobulk scRNA-seq data?
scrna-seq
rna-seq
log2fc
5 days ago by
JLee
• 0
0
votes
2
replies
227
views
how to evaluate SNPs that are regulating same gene expression across multiple tissues
snp
GTEx
updated 5 days ago by
LChart
3.3k • written 5 days ago by
rheab1230
▴ 140
1
vote
2
replies
238
views
GSEA Result Visualization in R
r
enrichplot
gsea
visualization
enrichResult
5 days ago by
Cortney
• 0
1
vote
2
replies
373
views
How to display all top markers in the heatmap by DoHeatmap (Seurat) when there are duplicates of top marker genes for several cell clusters
DoHeatmap
Seurat
5 days ago by
alwayshope
▴ 30
3
votes
2
replies
262
views
How to retrieve LoF and missense variants in WES data?
bcftools
variants
plink
SNPs
updated 5 days ago by
luffy
▴ 40 • written 5 days ago by
_quantum_girl_
▴ 10
0
votes
2
replies
270
views
How to find positions with higher depth relative to their surroundings
depth
python
samtools
updated 5 days ago by
xiaoguang
▴ 130 • written 5 days ago by
hyperdx1
• 0
3
votes
2
replies
323
views
Identifying common DEGs among multiple datasets
R
DEG
updated 5 days ago by
Barry Digby
★ 1.2k • written 5 days ago by
Shma
• 0
1
vote
2
replies
262
views
How to separate proteins on the same chain?
pdb
protein
updated 4 days ago by
Ram
40k • written 6 days ago by
Zayyan
▴ 10
8
votes
2
replies
2.9k
views
How to edit fasta headers to keep only ID and organism?
fasta
updated 4 days ago by
Ram
40k • written 3.0 years ago by
A_heath
▴ 140
3
votes
2
replies
274
views
Scanning for ultra-hot topics in science via pubmed, or using other tools
growth
pubmed
4 days ago by
LauferVA
3.7k
5
votes
2
replies
244
views
kallisto normalized TPM values without bootstraps
tpm
cibersort
sleuth
kallisto
RNA-seq
3 days ago by
butterman16
▴ 20
2
votes
2
replies
248
views
How to check RNAseq support for annotated genes?
gene
RNA-seq
annotation
updated 3 days ago by
Michael
53k • written 4 days ago by
BioinfoBee
• 0
1
vote
2
replies
456
views
Virtual box
virtual-machine
offtopic
updated 3 days ago by
Ram
40k • written 7 months ago by
georgeof35
• 0
0
votes
2
replies
262
views
Modify the code to take most abundant reads from a cluster and process it.
cd-hit-est
clustering
2 days ago by
Mo
▴ 40
1
vote
2
replies
272
views
Dotplot error: subscript out of bound
R
scRNA-seq
seurat
2 days ago by
Xuhao
• 0
3
votes
2
replies
355
views
How to create structural variants ground truth for alignment of two long-read genome assemblies?
yeast
assembly
structural-variation
SV-callers
2 days ago by
Thomas
▴ 20
1
vote
2
replies
268
views
Restricting vcf entries based on ID length
bcftools
vcf
vcftools
updated 1 day ago by
chrchang523
10k • written 18 days ago by
ethan.kreuzer
• 0
1
vote
2
replies
126
views
Is it normal if regress out the cell cycle effects but the DEGs are quite the similar (no big changes)
regress_out
Cell_cycle
Seurat
21 hours ago by
alwayshope
▴ 30
0
votes
2
replies
137
views
Visualize where kmers are on a reference genome
kmer
visualize
updated 18 hours ago by
Alex Reynolds
35k • written 19 hours ago by
Carrie
• 0
1
vote
2
replies
225
views
Understanding TCGA barcodes with dot in the fieldname
tcga
updated 12 hours ago by
Zhenyu Zhang
▴ 980 • written 3 days ago by
Tahsin
• 0
1
vote
2
replies
719
views
Job:
Scientist Position, Data Science AI/ML for Biology (JRD DS)
Data-Science
JNJ
Janssen
updated 12 hours ago by
Ram
40k • written 13 months ago by
Shicheng Guo
★ 9.3k
224 results • Page
3 of 5
Recent Votes
Comment: Calculation of TMB on gene level
Recommended way to normalize SmartSeq2 gene expression matrix to better match 10X expression data
Answer: Filter transcription factors
Comment: Quantification after transcriptome assembly with Trinity
Snakemake: output folder a as dependency to a different rule
A: Snakemake: output folder a as dependency to a different rule
A: In Seurat, How Do nCount_RNA Differ from nFeature_RNA?
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Recent Replies
Comment: bcftools error merging two VCFs: REF prefixes differ
by
iraun
6.1k
I can't find information with respect to the reference genome used to call the variants in `VCF_d`, but in `VCF_p` it seems they used GRCh3…
Comment: Calculation of TMB on gene level
by
smrutimayipanda
▴ 20
I am asking about TMB calculation on gene level, especially TCGA data
Comment: Calculation of TMB on gene level
by
smrutimayipanda
▴ 20
can you please tell me why it is technically incorrect?
Answer: Gene enrichment analysis of prokaryotes gene
by
dthorbur
▴ 550
[Here](https://github.com/golden75/prokaryote_RNASeq) is a tutorial on how to use the R package DESeq2 for prokaryotic RNAseq analyses. [H…
Comment: Read block operation failed with BAM file
by
John Marshall
3.0k
Indeed, though it is a seek issue when accessing files **over HTTP and other network protocols**. So, unless there's something you didn't m…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr
by
RM123
▴ 10
Thank you for your help. I am comparing 4 groups, but as I have gene expression data I have a considerable number of boxplots to make. I fo…
Comment: gene correlations in between two groups
by
ATpoint
76k
And how should I know this? I cannot read minds, nor see your screen, data or anything. Please ask a good question with necessary details. …
Comment: gene correlations in between two groups
by
edus_bioinfo
▴ 40
Thanks. But they are already analyzed. Afaik it analyzes raw data. In my dataset for each gene there is score. I want to interpret the data…
Answer: GWAS phenotype
by
dthorbur
▴ 550
Hello again. Yes, you can conduct GWAS using binary trait data, but it comes with a whole suite of complications. See [this](https://ww…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr
by
RM123
▴ 10
Hello Dariober, That seems like a good solution, however I'm pretty new to R. Could you tell me how I can do that?
Comment: how to create a loop in R
by
Nicolas Rosewick
10k
Not really a bioinformatics related question. Start by looking at R tutorial, there is plenty of them online e.g. : https://www.statmethods…
Comment: Violin plot (Monocle 3) - Troubleshooting
by
fracarb8
★ 1.2k
You did not add the screenshot.
Answer: BED files
by
Alex Reynolds
35k
Generically via `bedmap`: ``` bedmap --echo --echo-map --count exome.bed annotations.bed > answer.bed ``` The `annotations.bed` fil…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr
by
dariober
14k
It seems to me that anova followed by HSD is a more sensible approach than applying independent t-tests. Granted this is the first time I s…
Comment: BED files
by
barslmn
★ 1.8k
I am guessing you want the annotation files. https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/
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