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1,000 results • Page
5 of 20
Sort: Votes
Rank
Views
Votes
Replies
54
votes
52
replies
46k
views
12 follow
Tool:
Gene Set Clustering based on Functional annotation (GeneSCF)
geneSCF
Gene-Clustering
updated 3 months ago by
Ram
40k • written 9.2 years ago by
EagleEye
7.5k
54
votes
34
replies
4.2k
views
13 follow
Forum:
Should We Release Database Dumps Of All Questions On Biostar?
meta
biostars
updated 7 months ago by
Ram
40k • written 12.8 years ago by
Istvan Albert
98k
54
votes
24
replies
3.7k
views
12 follow
News:
Big news from Microsoft. BASH on windows.
windows
updated 5 months ago by
Ram
40k • written 7.5 years ago by
poisonAlien
★ 3.1k
54
votes
13
replies
9.9k
views
6 follow
Tool:
Bedtools: Analyzing Genomic Features
bedtools
updated 3 months ago by
Ram
40k • written 11.4 years ago by
Istvan Albert
98k
54
votes
7
replies
3.8k
views
6 follow
Tool:
Looking For People That Would Try A Custom Genome Viewer That I Wrote For Bioinformatics
genome-viewer
updated 3 months ago by
Ram
40k • written 10.4 years ago by
chbelhumeur2000
▴ 40
54
votes
16
replies
5.2k
views
13 follow
Forum:
The new era of bioinformatics: simple and fast tools, fewer and more informative data
kallisto
computational-cost
updated 8 months ago by
Ram
40k • written 8.4 years ago by
Istvan Albert
98k
54
votes
17
replies
5.2k
views
8 follow
Is annotation of enhancers to nearest gene pointless?
enhancer
annotation
updated 4 months ago by
Ram
40k • written 6.4 years ago by
BioinfGuru
★ 1.6k
53
votes
19
replies
42k
views
6 follow
Tutorial:
Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization
bigwig
chip-seq
rna-seq
updated 7 months ago by
Ram
40k • written 11.5 years ago by
Sukhi Singh
11k
53
votes
31
replies
5.8k
views
15 follow
Biostar Flyer For Outreach
biostars
updated 7 months ago by
Ram
40k • written 12.9 years ago by
Mary
11k
53
votes
30
replies
12k
views
8 follow
How to get sample names and genotype for SNP in multi-sample VCF file
SNP
genotype
GATK
updated 6 months ago by
AMARU
• 0 • written 5.6 years ago by
hellbio
▴ 510
53
votes
27
replies
3.8k
views
11 follow
Should General Programming Questions Actually Be Posted To Biostar?
meta
biostars
updated 7 months ago by
Ram
40k • written 12.2 years ago by
Pablo Pareja
★ 1.6k
53
votes
13
replies
5.1k
views
6 follow
Tool:
I made a DNA/gene/bioinformatics-y workshop for 11-16 year olds which people may find useful
school-outreach
updated 8 months ago by
Ram
40k • written 8.3 years ago by
Daniel
★ 3.9k
53
votes
11
replies
26k
views
10 follow
Out Of Disk Space With Picard Tools ?
picard
updated 3 months ago by
Ram
40k • written 11.5 years ago by
Gabriel R.
★ 2.9k
52
votes
14
replies
40k
views
13 follow
Converting Bam To Fastq
next-gen-sequencing
fastq
updated 3 months ago by
Ram
40k • written 13.5 years ago by
Zach Stednick
▴ 660
52
votes
11
replies
36k
views
8 follow
Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
RNA-Seq
updated 8 months ago by
Ram
40k • written 9.2 years ago by
thisismytest3023
▴ 210
52
votes
21
replies
47k
views
11 follow
Fastq Splitter For Paired End Reads
rna
updated 3 months ago by
Ram
40k • written 11.5 years ago by
Geparada
★ 1.5k
52
votes
18
replies
6.0k
views
14 follow
Forum:
Do You Feel Good Or Bad About Putting Your Photo At Biostar?
meta
biostars
updated 7 months ago by
Ram
40k • written 10.0 years ago by
ugly.betty77
★ 1.1k
52
votes
8
replies
4.5k
views
8 follow
Forum:
What Is The Proper Way To Think About Reinventing The Wheel As A Bioinformatician?
software-development
updated 7 months ago by
Ram
40k • written 10.6 years ago by
KCC
★ 4.1k
51
votes
16
replies
5.3k
views
11 follow
Forum:
What Are The Most Influential Bioinformatics/Computational Biology Papers Of 2011?
papers
updated 7 months ago by
Ram
40k • written 11.8 years ago by
Farhat
★ 2.9k
51
votes
10
replies
2.9k
views
6 follow
Is Biostar A Research Advice Tool Or A Tutor (Helping Students) Or Both?
meta
biostars
homework
updated 7 months ago by
Ram
40k • written 12.6 years ago by
Larry_Parnell
16k
51
votes
17
replies
3.5k
views
News:
Biostars 3.0 is now under testing. It has groups, charms and other interesting features.
meta
biostars
updated 7 months ago by
Ram
40k • written 8.5 years ago by
Istvan Albert
98k
51
votes
3
replies
22k
views
Tutorial:
Sam File Format - Lesser Known Tips And Tricks
sam
updated 7 months ago by
Ram
40k • written 10.7 years ago by
Ya
▴ 300
50
votes
20
replies
5.4k
views
18 follow
Forum:
Explain bioinformatics to a 10 year old
bioinformatics
updated 6 months ago by
Ram
40k • written 7.6 years ago by
novice
★ 1.1k
50
votes
17
replies
37k
views
17 follow
How To Get Number Of Reads In Bam File Efficiently In Python?
python
samtools
next-gen
sequencing
updated 11 months ago by
Ram
40k • written 13.2 years ago by
User 9996
▴ 840
50
votes
4
replies
8.6k
views
Forum:
How to add images to a Biostars post
how-to
7 months ago by
Ram
40k
50
votes
19
replies
4.5k
views
7 follow
Forum:
Proposal: Biostar Wants To Run Your Ads. Feedback Requested.
biostars
updated 7 months ago by
Ram
40k • written 10.6 years ago by
Istvan Albert
98k
50
votes
1
reply
7.4k
views
Tutorial:
Basic normalization, batch correction and visualization of RNA-seq data
edger
RNA-seq
updated 7 months ago by
Ram
40k • written 3.0 years ago by
ATpoint
77k
50
votes
15
replies
65k
views
12 follow
Sequence Number Count In Fastq.Gz File
counts
sequence
fastq
updated 7 months ago by
Ram
40k • written 12.3 years ago by
Bioscientist
★ 1.7k
50
votes
15
replies
29k
views
10 follow
Where To Download Pam50 Gene Set?
cancer
annotation
classification
updated 11 weeks ago by
DareDevil
★ 3.3k • written 10.2 years ago by
user
▴ 940
50
votes
16
replies
13k
views
12 follow
Tool:
Omictools: A didactic directory for omic data analysis (NGS, microarray, PCR, MS, NMR)
pcr
software
ngs
updated 3 months ago by
Ram
40k • written 10.0 years ago by
arnaud.desfeux
▴ 450
50
votes
18
replies
34k
views
12 follow
ATAC-seq peak calling with MACS
atac-seq
macs
ChIP-Seq
peaks
updated 3 months ago by
Ram
40k • written 7.1 years ago by
igor
13k
50
votes
10
replies
21k
views
9 follow
How Important Is Bioinformatics And How To Make A Case For It?
subjective
education
updated 7 months ago by
Ram
40k • written 12.4 years ago by
Allpowerde
★ 1.3k
50
votes
15
replies
16k
views
9 follow
Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. genome average)
sequencing
next-gen
ChIP-Seq
genome
gene
updated 11 months ago by
Ram
40k • written 8.7 years ago by
chemcehn
▴ 210
50
votes
14
replies
75k
views
10 follow
Tutorial:
Using R in Conda
R
updated 6 months ago by
Ram
40k • written 3.2 years ago by
rohitsatyam102
▴ 750
50
votes
3
replies
4.4k
views
Tutorial:
[[ Please read before posting a question ::: How To Ask A Good Question ]]
how-to
updated 6 months ago by
Ram
40k • written 4.7 years ago by
ATpoint
77k
50
votes
8
replies
9.3k
views
6 follow
Forum:
Encode Commentary From Dan Graur
encode
updated 7 months ago by
Ram
40k • written 10.6 years ago by
Damian Kao
16k
50
votes
23
replies
21k
views
13 follow
intersect VCF files
VCF
updated 7 months ago by
Ram
40k • written 7.6 years ago by
Bogdan
★ 1.4k
49
votes
36
replies
7.8k
views
11 follow
Forum:
New features and bug fixes for Biostar to work on during Google Summer of Code
meta
biostars
gsoc
updated 7 months ago by
Ram
40k • written 9.4 years ago by
Paolo
▴ 110
49
votes
27
replies
6.5k
views
10 follow
Forum:
Possible augmented reality tools for bioinformatics and current problems
visualization
3D
augmented-reality
updated 6 months ago by
Ram
40k • written 7.9 years ago by
Peter Leontev
▴ 90
49
votes
21
replies
3.8k
views
11 follow
How can I learn how to create a bioinformatics pipeline?
pipeline
updated 7 months ago by
Istvan Albert
98k • written 11 months ago by
Jean
▴ 50
49
votes
18
replies
7.5k
views
10 follow
What Is Bioinformatics?
subjective
updated 7 months ago by
Ram
40k • written 12.6 years ago by
Egon Willighagen
5.4k
49
votes
7
replies
11k
views
7 follow
Tutorial:
Genome Assembly Review Papers
assembly
papers
updated 7 months ago by
Ram
40k • written 11.1 years ago by
Istvan Albert
98k
49
votes
28
replies
26k
views
12 follow
Trimming A Fastq File Representing Rna-Seq Data
fastq
RNA-seq
updated 6 months ago by
Ram
40k • written 11.5 years ago by
Varun Gupta
★ 1.3k
49
votes
19
replies
6.8k
views
13 follow
Forum:
Why Are There No Proteomics Questions In Biostar?
proteomics
biostars
updated 7 months ago by
Ram
40k • written 12.9 years ago by
Jdnavarro
▴ 410
49
votes
13
replies
52k
views
13 follow
Calculating TPM from featureCounts output
RNA-Seq
updated 2 days ago by
camillab.
▴ 140 • written 7.7 years ago by
nash.claire
▴ 490
49
votes
6
replies
17k
views
Decoy In Reference Assembly
1000genomes
updated 4 months ago by
kmzhou4
• 0 • written 10.3 years ago by
Sangwoo Kim
▴ 420
48
votes
24
replies
7.6k
views
14 follow
Tool:
Hera: A new tool for RNA-Seq analysis
kallisto
RNA-Seq
STAR
gene-fusion
updated 3 months ago by
Ram
40k • written 6.2 years ago by
sonpham
▴ 580
48
votes
16
replies
5.0k
views
12 follow
Bio-Informatics Results Supporting Ongoing Evolution
evolution
publication
written 12.8 years ago by
Monzoor
▴ 310
48
votes
18
replies
29k
views
16 follow
extract only geneID and gene symbol from GTF file
gtf
python
genome
updated 7 months ago by
Ram
40k • written 8.4 years ago by
catherine
▴ 250
48
votes
38
replies
16k
views
8 follow
Forum:
Eukaryotic Genome Annotation in 2016
software
genome
annotation
updated 5 months ago by
Ram
40k • written 7.6 years ago by
Eric Normandeau
11k
1,000 results • Page
5 of 20
Recent Votes
A: running RAxML and MrBayes over concatinated multiple sequence alignments
Comment: Weirdness in annotation (missing allele frequencies)
Comment: Weirdness in annotation (missing allele frequencies)
Comment: ncbi error report log for validate fastq issue
Comment: ncbi error report log for validate fastq issue
A: Bowtie2 MAPQ difference using local vs end-to-end alignment
C: Bowtie2 MAPQ difference using local vs end-to-end alignment
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Recent Replies
Comment: Weirdness in annotation (missing allele frequencies)
by
Jeremy Leipzig
21k
0.60625 is 97/160 so if you have 80 individuals in your VCF that's an internal allele frequency, not gnomAD
Comment: Weirdness in annotation (missing allele frequencies)
by
Can Abdullah
• 0
Yes, I was confused as well. I think the same. Maybe Annovar uses some other resources besides gnomad, but it does not make sense. Also, I …
Comment: Weirdness in annotation (missing allele frequencies)
by
Can Abdullah
• 0
Thank you so much, I decided to move forward as you suggested. Initially, I thought using the most up-to-date databases and positions would…
Comment: Getting the overlap between two GTF files
by
GenoMax
134k
Something in `AGAT` should work: https://agat.readthedocs.io/en/latest/?badge=latest
Answer: Automate the Splitting of a VCF File by Sample (bcftools)
by
Pierre Lindenbaum
157k
> My problem has been with trying to loop the process. ok here is a **nextflow** based solution,(NOT tested) workflow { …
Comment: Assessing Rockhopper's output
by
langziv
▴ 50
I see. I tried using the GUI Rockhopper for RNA-seq analysis of a K. pneumoniae strain, but the program didn't find the strain's assembly…
Answer: Getting the overlap between two GTF files
by
Pierre Lindenbaum
157k
bedtools intersect \ -a <(awk '/^[^#]/ {printf("%s\t%d\t%s\t%s\n",$1,int($4)-1,$5,$0);}' file1.gtf | sort -t $'\t' -k1,1 -k2…
Comment: Assessing Rockhopper's output
by
shelkmike
▴ 980
I used Rockhopper only for bacterial genomes assembled into circular contigs or circular scaffolds.
Comment: Unable to install HorvathMammalMethylChip40manifest packages
by
ATpoint
77k
There is no package of that name in CRAN or Bioconductor. Where do you have it from, so which tutorial you follow?
Comment: Subclustering of intergated cells from scRNA-seq data
by
fifty_fifty
▴ 60
thank you. This is exactly what I was looking for
Answer: Search RCSB with a list of protein names?
by
Mensur Dlakic
★ 25k
This is not the most elegant solution, but it should work with previous suggestions. In this remote directory: http://ftp.wwpdb.org/p…
Answer: Automate the Splitting of a VCF File by Sample (bcftools)
by
Ram
40k
The manual says you can split samples out at once using the `+split` plugin. So, `bcftools +split -Oz -o <PATH> file.vcf.gz` should do the …
Comment: differences between trajectories in conditions with Monocle3 or other tools
by
Amitm
★ 2.2k
Phate (or Monocle) doesn't do UMAP. If you have done UMAP already (using seurat) then you could use the cell barcode to UMAP cluster label …
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti
by
Y
• 0
I figured out how to make it work. The bams have to be comma separated not just by space: cd "${input_directory_with_associated_bam_fi…
Comment: Search RCSB with a list of protein names?
by
Joseph
• 0
Hey, this is so close to what I'm looking for - I clarified in my edit. This is a great way to batch download lots of PDBs in RCSB by their…
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