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1,000 results • Page 3 of 20
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80
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34
replies
4.5k
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11 follow
Forum: Authorship issues- how to resolve?
authorship
updated 8 months ago by 40k • written 8.3 years ago by ▴ 520
15
votes
34
replies
11k
views
Improving efficiency of awk for large files
awk
updated 11 months ago by 40k • written 8.2 years ago by ▴ 350
146
votes
34
replies
53k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music cancer tcga mutation maf
updated 7 months ago by 40k • written 10.5 years ago by 6.0k
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 40k • written 12.8 years ago by 98k
100
votes
33
replies
105k
views
23 follow
How To Split A Bam File By Chromosome
bam split chromosome
updated 2 days ago by • 0 • written 11.3 years ago by ▴ 390
27
votes
33
replies
3.2k
views
7 follow
Forum: Biostars question catagories
statistics biostars meta
updated 5 months ago by 40k • written 7.0 years ago by 13k
10
votes
33
replies
3.1k
views
Looking for a tool like fastq screen but for ONT data
gridion nanopore ont minion
updated 3 months ago by 40k • written 5.2 years ago by ★ 1.4k
16
votes
33
replies
7.5k
views
9 follow
Back-filling missing genotypes in merged VCF
vcf
updated 9 months ago by 157k • written 8.9 years ago by ★ 1.1k
135
votes
33
replies
60k
views
19 follow
VCF files: Change Chromosome Notation
vcf next-gen sequence
updated 11 months ago by 40k • written 9.4 years ago by ▴ 480
288
votes
33
replies
99k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 7 months ago by 40k • written 9.9 years ago by 20k
120
votes
33
replies
37k
views
24 follow
Forum: Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 4 months ago by ★ 2.4k • written 10.1 years ago by 11k
82
votes
32
replies
7.0k
views
13 follow
Forum: Shall We Go Back To Stackexchange?
meta
updated 7 months ago by 40k • written 10.9 years ago by ★ 3.6k
18
votes
31
replies
7.1k
views
How can I easily remove overlapping transcripts, keeping only longest transcript, in a GFF file.
gff parse
updated 6 months ago by 8.2k • written 5.0 years ago by ▴ 350
53
votes
31
replies
5.8k
views
15 follow
Biostar Flyer For Outreach
biostars
updated 7 months ago by 40k • written 12.9 years ago by 11k
13
votes
31
replies
5.8k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
geneset genome gene abinitio
updated 6 months ago by 40k • written 4.1 years ago by 8.2k
9
votes
31
replies
12k
views
6 follow
How to concatenate multiple fasta file
sequence genome
updated 4 months ago by • 0 • written 5.1 years ago by ▴ 40
59
votes
31
replies
4.1k
views
12 follow
News: Example of how bioinformaticians can publish in Scientific Reports (by nature publishing group) using publicly available NGS data
publication NGS
updated 5 months ago by 40k • written 6.7 years ago by 10k
78
votes
31
replies
6.2k
views
14 follow
Forum: Do Bad Questions Even Exist?
biostars general education
updated 7 months ago by 40k • written 12.6 years ago by 10k
30
votes
31
replies
3.1k
views
11 follow
Forum: I need your help to find my future
internship masters career
updated 5 months ago by 40k • written 7.2 years ago by ▴ 90
38
votes
31
replies
2.3k
views
10 follow
Forum: To the Biologists out there: What bioinf tool are you missing?
education career
updated 5 months ago by 40k • written 7.2 years ago by ▴ 180
146
votes
31
replies
132k
views
26 follow
Useful Bash Commands To Handle Fasta Files
command-line fasta bash
updated 9 weeks ago by 40k • written 11.6 years ago by ★ 2.9k
28
votes
31
replies
5.1k
views
8 follow
Forum: Biostar Ads Are Now Live. Feedback And Comments Are Sought.
biostars
updated 7 months ago by 40k • written 10.3 years ago by 98k
31
votes
30
replies
14k
views
6 follow
Tool: BioVinci: user-friendly software to make plotting easy - PCA, 3D scatter plot, venn diagram, you name it.
gene RNA-Seq Venn-diagram PCA
updated 3 months ago by 40k • written 5.4 years ago by ▴ 450
102
votes
30
replies
60k
views
25 follow
Tools To Find Gene Ontology Term Enrichment
gene enrichment
updated 3 months ago by 40k • written 13.6 years ago by ★ 1.0k
18
votes
30
replies
9.3k
views
6 follow
Tool: Introducing FilterByTile: Remove Low-Quality Reads Without Adding Bias
Illumina BBMap filterbytile
updated 3 months ago by 40k • written 6.8 years ago by 18k
47
votes
30
replies
3.8k
views
10 follow
Forum: Bioinformatics software distribution
software
updated 4 months ago by 40k • written 6.6 years ago by ★ 2.7k
37
votes
30
replies
4.4k
views
7 follow
Forum: Spam In Rss Feeds
meta RSS
updated 7 months ago by 40k • written 10.7 years ago by 5.3k
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 • 0 • written 5.6 years ago by ▴ 510
34
votes
30
replies
2.3k
views
6 follow
Tool: BioFlows - Container-enabled Bioinformatics pipeline engine
workflow next-gen RNA-Seq pipeline
updated 6 months ago by 40k • written 2.8 years ago by ▴ 90
61
votes
29
replies
6.9k
views
14 follow
Best bioinfo one-liners?
linux
updated 8 months ago by 40k • written 8.4 years ago by 4.1k
84
votes
29
replies
30k
views
20 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 9 weeks ago by • 0 • written 7.6 years ago by 20k
86
votes
29
replies
9.1k
views
9 follow
Forum: What is the future of EMBL-EBI (and European bioinformatics in general) in case of a 'Brexit'?
EU brexit EBI politics
updated 5 months ago by 40k • written 7.3 years ago by 53k
275
votes
29
replies
267k
views
25 follow
How To Filter Mapped Reads With Samtools
samtools
updated 10 months ago by 40k • written 10.9 years ago by ▴ 630
64
votes
29
replies
15k
views
15 follow
Forum: Fundamentals Of Designing Biological Databases?
database
updated 7 months ago by 40k • written 12.9 years ago by ▴ 130
73
votes
29
replies
3.9k
views
12 follow
Tool: ChatGPT optimized for bioinformatics questions
gpt
11 weeks ago by Sasha ▴ 720
33
votes
29
replies
19k
views
12 follow
Large File Transfers Of Ngs Data: Rsync / Bbcp / Unison / What?
data
updated 9 months ago by 40k • written 10.2 years ago by ▴ 110
63
votes
28
replies
3.4k
views
11 follow
Forum: Bioinformatics analyses & errors: need for better post-publication tools?
next-gen RNA-Seq
updated 5 months ago by 40k • written 7.4 years ago by ★ 1.2k
33
votes
28
replies
11k
views
9 follow
Is There Any Reference Exome ?
exome next-gen-sequencing
updated 9 months ago by 40k • written 12.5 years ago by 18k
2
votes
28
replies
1.2k
views
how do I generate frame 5 and 6 from the complementary strand?
python
updated 5 months ago by 40k • written 5 months ago by • 0
49
votes
28
replies
26k
views
12 follow
Trimming A Fastq File Representing Rna-Seq Data
fastq RNA-seq
updated 6 months ago by 40k • written 11.5 years ago by ★ 1.3k
60
votes
28
replies
7.6k
views
27 follow
Forum: Jim Robinson of the Integrative Genomics Viewer (IGV) uses this
uses-this
updated 6 months ago by 40k • written 9.0 years ago by 98k
19
votes
28
replies
14k
views
8 follow
Subsample BAM to fixed number of alignments
subsampling bam
updated 9 months ago by 40k • written 8.3 years ago by ★ 3.9k
48
votes
28
replies
8.6k
views
9 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
4 months ago by Ram 40k
18
votes
27
replies
18k
views
20 follow
Where Can I Download Vcf Files For Publicly Available Data?
vcf snp
updated 6 months ago by 40k • written 11.8 years ago by ▴ 640
65
votes
27
replies
6.7k
views
14 follow
Forum: What is the reason for most software errors in Bioinformatics according to you?
software-error blast sequencing SNP R
updated 5 months ago by 40k • written 7.5 years ago by ▴ 110
3
votes
27
replies
2.0k
views
7 follow
Forum: What server do you use?
HPC AWS
updated 4 months ago by 40k • written 5.2 years ago by ★ 1.8k
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 40k • written 7.9 years ago by ▴ 90
30
votes
27
replies
2.2k
views
11 follow
Forum: How do you spend your time (productively) when your script is running?
time-management
updated 5 months ago by 40k • written 6.6 years ago by 7.1k
63
votes
27
replies
26k
views
18 follow
Data Too Big To Be Stored In Memory: Common Options
python
updated 7 months ago by 40k • written 10.9 years ago by ▴ 720
197
votes
27
replies
32k
views
20 follow
Forum: Bioinformatics Cartoon
bioinformatics
updated 11 weeks ago by 40k • written 11.7 years ago by ★ 2.3k
1,000 results • Page 3 of 20
Recent Votes
A: .gstmp extension on .bam files downloaded from google bucket; and EOF marker is
Comment: Significance testing of top vs. random SNPs
Answer: Search RCSB with a list of protein names?
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
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Recent Replies
Comment: MAKER: WARNING: Could not get initialization lock. Trying Again... by GenoMax 134k
What kind of hardware are you running this on? You need to have the right kind of hardware (multiple CPU's not just cores), MPI libraries a…
Answer: Getting the overlap between two GTF files by Alex Reynolds 35k
Using `bedops --intersect` and `gtf2bed` will get their common genomic space: ``` bedops --intersect <(gtf2bed < transcripts.gtf) <(gtf2be…
Comment: Encountering Error while Running 'make vcf' in Biostar Handbook by Tully • 0
```bash # Obtain the makefile curl -s http://data.biostarhandbook.com/make/snpcall.mk > Makefile # Run the makefile make vcf ``` Error me…
Comment: Encountering Error while Running 'make vcf' in Biostar Handbook by Tully • 0
> System Information: Ubuntu 22.04 (WSL2) > > Shell: zsh > > Installation Verification: Yes, doctor.py OK [1]: https://www.biostarhand…
Comment: Retrieve The Reads And Fastq From Bam File by Reem • 0
Did it affect the bamtofastq output file? if so how did you solve the problem? Thanks
Answer: How to import bigwig files into igvR by Trivas ★ 1.5k
You could try seeing if this fixes your issue with rtracklayer: https://support.bioconductor.org/p/p133244/
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?
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