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353 results • Page
2 of 8
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Views
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0
votes
8
replies
416
views
STAR aligner options
STAR
12 hours ago by
theophile
• 0
3
votes
3
replies
408
views
I can't add VAF from population for all of my variants from VCF file
genomics
vcf
gnomad
updated 16 days ago by
Ram
43k • written 17 days ago by
Samuel
▴ 20
1
vote
5
replies
408
views
Haddock 2.4
Protein
Docking
updated 8 days ago by
dthorbur
★ 1.7k • written 10 days ago by
Preeti
• 0
0
votes
6
replies
406
views
Download Panther entry list
PANTHER
6 days ago by
Nicolas
• 0
0
votes
5
replies
405
views
Deeptools scale issue for plotHeatmap
deeptools
computeMatrix
plotHeatmap
6 days ago by
Learner
• 0
0
votes
5
replies
390
views
Same NCBI IDs for different Ensembl IDs / Multiple NCBI IDs for an Ensembl ID
KEGG
ENTREZ
ENSEMBL
15 days ago by
Maxwell
▴ 20
0
votes
7
replies
389
views
Error "ckalloc: request for negative space" about multiz
multiz
23 days ago by
marh32
• 0
0
votes
0
replies
384
views
Error in validObject(.Object) : invalid class “ExpressionSet” object: sampleNames differ between assayData and phenoData
GSVA
27 days ago by
Chris
▴ 260
0
votes
0
replies
378
views
Any tool that can give me a list of DNA/RNA aptamers against specific protein as the in vitro SELEX library to screen the sequences?
aptamer
protein
SELEX
29 days ago by
J.F.Jiang
▴ 910
1
vote
5
replies
374
views
Is there a reason why fastq files from SRAExplorer and SRAToolkit are different sizes?
sraexplorer
sratoolkit
updated 16 days ago by
GenoMax
140k • written 19 days ago by
biotrekker
▴ 100
0
votes
0
replies
372
views
Guidance Needed: Matching Cancer-Specific Alterations with ATAC-seq Genomic Coordinates
Alignment
ATAC-seq
Cancer
17 days ago by
davoudamirimehr
• 0
0
votes
1
reply
370
views
Strange distribution of logFC values after searching for significantly differentially expressed genes
limma
23 days ago by
Robert
• 0
0
votes
6
replies
369
views
why the file is low after combining the Hi-C reads using Arima genomics pipeline of mapping
bwa
mapping
genome
samtools
plants
20 days ago by
rj.rezwan
• 0
0
votes
6
replies
366
views
Contamination in my FASTQC files
Fastqc
bowtie2
20 days ago by
carlosgonzalezcruz327
▴ 20
0
votes
0
replies
362
views
SNV occuring 2 fold more in forward than in reverse reads should be filtered?
Variant-Calling
updated 2 days ago by
Ram
43k • written 2.2 years ago by
jeni
▴ 90
0
votes
5
replies
362
views
Issues with bcftools
Bcftools
updated 21 days ago by
Pierre Lindenbaum
160k • written 21 days ago by
hgrsce
• 0
0
votes
2
replies
358
views
How can I have the structure of a gene (or haplotypes of a gene) on the top of the LD plot on Haploview
LDplot
Haploview
HaplotypeBlocks
LinkageFormat
21 days ago by
mona.patoughi
• 0
0
votes
4
replies
357
views
Can I perform a Functional Enrichment Analysis on a specific list of pre-defined genes?
RNA-seq
DGE
11 days ago by
Adam
• 0
0
votes
5
replies
350
views
loop string set
python
stringset
updated 22 days ago by
rpolicastro
13k • written 24 days ago by
aj123
▴ 120
1
vote
5
replies
346
views
How to normalise RNA seq data from two independent experiments to the same scale.
RNAseq
updated 22 days ago by
jv
★ 1.7k • written 23 days ago by
Mo
▴ 40
0
votes
4
replies
339
views
Dsuite Dinvestigate error but no indication as to the source
Dsuite
20 days ago by
Drew
• 0
0
votes
0
replies
336
views
Benchmarking pipeline for Variant identification using RNA-seq data
RNA-seq
somatic
Variant-calling
germline
updated 2 days ago by
Ram
43k • written 17 months ago by
ahkam.s
• 0
0
votes
3
replies
333
views
Tools and software to visualize the moving cell compartments in 3D
3D-visualization
cell-compartments
20 days ago by
saamar.rajput
▴ 70
2
votes
2
replies
332
views
Would you recommend me any tool to assign protein family membership to an aminoacidic fasta file?
protein-annotation
fasta
updated 8 days ago by
Dunois
★ 2.5k • written 7 weeks ago by
v.berriosfarias
▴ 140
0
votes
4
replies
330
views
PCA Plot in Single-cell RNA-seq Data
RNA-seq
PCA
single
cell
29 days ago by
Darya
• 0
0
votes
7
replies
323
views
single nuclei sequencing questions
fastq
single-nuclei-sequencing
updated 20 days ago by
Ram
43k • written 20 days ago by
Long
• 0
2
votes
3
replies
321
views
Spearman correlation for ATAC data
correlation
Spearman
updated 29 days ago by
gglim
▴ 140 • written 4 weeks ago by
daffodil
▴ 10
0
votes
7
replies
318
views
Salmon Quantification in Alignment based-mode
Salmon
RNA-seq
TPM
updated 22 hours ago by
GenoMax
140k • written 1 day ago by
Patadu94
• 0
0
votes
5
replies
312
views
Parsing fasta file by coordinates
linux
fasta
updated 4 hours ago by
GenoMax
140k • written 3 days ago by
sorrymouse
▴ 120
0
votes
2
replies
311
views
Alphafold2 Colab
AlphaFold
updated 24 days ago by
dthorbur
★ 1.7k • written 26 days ago by
Preeti
• 0
0
votes
2
replies
305
views
BMI as a continuous variable is my outcome, which type data i should put to calculate
transcriptomics
29 days ago by
jiefei
• 0
1
vote
4
replies
300
views
Differential analysis using R
DNA
methylation
updated 23 days ago by
Michael
54k • written 23 days ago by
maryak
▴ 20
3
votes
4
replies
299
views
What should be used as a "baseline" in pooled CRISPR screen?
CRISPR
MAGECK
FACS
20 days ago by
Aleksandr
▴ 10
0
votes
3
replies
298
views
How to proceed with downstream analysis after tumor-only snp calling using Varscan2?
snv
compressing
varscan
bcftools
6 days ago by
kabir.deb
▴ 80
2
votes
2
replies
292
views
Seeking help with Tcga Target Gtex Expected Count Data
R
TCGA
gTEX
5 days ago by
bioinfo_enthusiast
• 0
4
votes
6
replies
291
views
Protein loops
protein
Loop
14 days ago by
Curious
▴ 10
0
votes
2
replies
291
views
DiffBind issue in identification of differentially enriched peaks between two conditions
DiffBind
ChIP-Seq
22 days ago by
accibio
▴ 20
0
votes
5
replies
290
views
Bedtools getfasta: error
getfasta
bedtools
updated 17 days ago by
GenoMax
140k • written 17 days ago by
ummeswaiba
• 0
0
votes
2
replies
289
views
PopGenome lost individual information
PopGenome
2 days ago by
Yixuan
• 0
5
votes
3
replies
287
views
samtools view: error reading file
samtools
bowtie2
updated 22 days ago by
bioinfo_ga
▴ 70 • written 24 days ago by
ray
• 0
1
vote
3
replies
287
views
FastQC on nanopore data: high proportion of polyA and polyG. Why ?
fastQC
polyG
ONT
nanopore
polyA
updated 16 days ago by
GenoMax
140k • written 16 days ago by
Matt
• 0
1
vote
2
replies
286
views
How to extract mutations in a particular gene from the VCF file of whole genome
NGS
mutations
VCF
21 days ago by
saamar.rajput
▴ 70
1
vote
1
reply
278
views
Advice for genetic diversity stats analysis with both variant and variant sites
pi
diversity
vcf
genetics
updated 7 days ago by
dthorbur
★ 1.7k • written 8 days ago by
ekirsch
• 0
1
vote
11
replies
276
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
updated 4 hours ago by
GenoMax
140k • written 10 hours ago by
Lila M
★ 1.2k
1
vote
2
replies
274
views
Deseq2 shows differential expression while TPM values are not significantly different
Deseq2
TPM
updated 29 days ago by
jv
★ 1.7k • written 29 days ago by
Aiswarya
▴ 10
1
vote
3
replies
272
views
RNA-seq bam file normalization
RNA-seq
bam
normalization
updated 22 days ago by
dsull
★ 5.7k • written 24 days ago by
maplewj
▴ 10
3
votes
2
replies
271
views
Seeking Guidance on How to Annotate Unusual Cell Populations in Single-Cell Data
Transcriptomics
Annotation
Single
Bioinformatics
Cell
27 days ago by
Daddy
▴ 20
0
votes
3
replies
270
views
bioinformatics
bioinformatics
updated 22 days ago by
GenoMax
140k • written 22 days ago by
reachedahead225
• 0
0
votes
2
replies
270
views
JASPAR2024_getMatrixSet error
getMatrixSet
JASPAR2024
updated 2 days ago by
Ram
43k • written 5 weeks ago by
maplewj
▴ 10
1
vote
4
replies
269
views
Some questions about bulk RNA-seq data normalization
RNA-seq
NGS
bulk
normalize
16 days ago by
feather-W
• 0
353 results • Page
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Comment: Error in openning FastQC
by
friszd
• 0
after running fastqc -o output.html input.fastq, terminal returns: " Specified output directory 'output.html' does not exist " , when i run…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
The question you should be looking into is why the Q scores are dropping there? Are there `N` calls indicating some issue with that cycle?
Comment: Error in openning FastQC
by
GenoMax
140k
What is `ctrl+c ctrl+v`? You may actually be killing the running fastqc process. If you run `fastqc` interactively (like what was shown ab…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Dave Carlson
★ 1.7k
Ugh. I've definitely done this one before as well. And was none too happy about it.
Comment: Error in openning FastQC
by
friszd
• 0
fastqc -o output.html input.fastq ctrl+c ctrl+v
Comment: Error running local blastn in R using system2
by
GenoMax
140k
What do you see if you `cat nt_euk.nal`? Do the number of pieces mentioned in that file match with what you locally have?
Comment: Low number of both surviving reads after trimming
by
GenoMax
140k
It is your data and if you want to do that it is up to you. You may be throwing away essentially good data (you should remove the nextera s…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Istvan Albert
100k
Some things never change ... the most common mistake is still the one on top there
Comment: Low number of both surviving reads after trimming
by
Ram
43k
I see that the code content was not added again, just the formatting modified. The output is still mangled. Compare it to the output you se…
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Mensur Dlakic
★ 26k
I was trying to avoid re-living traumatic events, but here goes. This is an attempt to delete all the files with a certain extension but in…
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Thank you for your response. There was no particular reason of `LEADING:20 and TRAILING:20`, but I used the same parameters as I had used …
Comment: Low number of both surviving reads after trimming
by
GenoMax
140k
A significant fraction of your reads appear to have the nextera sequence, that combined to this directive `LEADING:20` (do you have a reaso…
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Here is my fastqc, especially adapter content graph, before trimming(R1 and R2): ![enter image description here][1] And this after trimm…
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Thanks, I modified.
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Pierre Lindenbaum
160k
11 years ago: https://www.biostars.org/p/7126/
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