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Forum: Nextseq for analysts
basespace casava bcl2fastq nextseq
updated 6 months ago by 40k • written 9.3 years ago by 5.3k
42
votes
21
replies
14k
views
10 follow
Forum: A Database Of Signatures Of Selection In The 1000 Genomes Dataset
1000genomes human selection
updated 6 months ago by 40k • written 9.6 years ago by 28k
99
votes
21
replies
8.3k
views
14 follow
Forum: How Has Bioinformatics Improved Over Time?
bioinformatics
updated 7 months ago by 40k • written 10.7 years ago by ▴ 370
27
votes
21
replies
8.3k
views
9 follow
Forum: Better for my career: Degree in computer science or Phd in bioinformatics?
computer-science phd
updated 5 months ago by 40k • written 7.0 years ago by ★ 1.6k
66
votes
21
replies
6.1k
views
18 follow
Forum: Is there anyone who was a pure biologist?
next-gen
updated 6 months ago by 40k • written 9.4 years ago by ▴ 100
35
votes
21
replies
2.6k
views
11 follow
Forum: Should you restrict use of your software based on your political views?
software
updated 12 months ago by 40k • written 8.0 years ago by 26k
81
votes
21
replies
4.5k
views
16 follow
Forum: [UPDATE] Thrown into a Bioinformatics Position
bioinformatics
updated 6 months ago by 40k • written 7.3 years ago by ★ 3.2k
36
votes
21
replies
17k
views
9 follow
Forum: What Is Your Favorite Conserved Protein?
protein conservation
updated 6 months ago by 40k • written 10.1 years ago by 11k
37
votes
21
replies
11k
views
10 follow
Forum: Orientation of PE reads a review of --fr --ff and --rf meanings
RNA-Seq
updated 4 months ago by 40k • written 4.9 years ago by 8.2k
67
votes
21
replies
5.5k
views
8 follow
Forum: Meta: Markdown in Biostars (now enabled)
meta
6 months ago by Ram 40k
20
votes
21
replies
2.5k
views
6 follow
Forum: Next Gen seq for Job interview
next-gen
updated 6 months ago by 40k • written 8.6 years ago by ▴ 20
17
votes
21
replies
3.1k
views
8 follow
Forum: bioinformatics thesis
thesis
updated 2.4 years ago by 21k • written 2.5 years ago by ▴ 40
29
votes
21
replies
5.6k
views
Forum: PhD vs Field application scientist in industry
career
updated 5 months ago by 40k • written 7.1 years ago by ▴ 80
12
votes
20
replies
2.8k
views
Forum: Starting a career in Bioinformatics
career
updated 6 months ago by 40k • written 7.3 years ago by ▴ 10
91
votes
20
replies
19k
views
15 follow
Forum: Publications for individualized medicine in cancer by whole genome, exome or transcriptome sequencing
N-of-one WGS RNA-Seq next-gen Exome
updated 11 months ago by 40k • written 9.4 years ago by 20k
50
votes
20
replies
5.4k
views
18 follow
Forum: Explain bioinformatics to a 10 year old
bioinformatics
updated 6 months ago by 40k • written 7.5 years ago by ★ 1.1k
42
votes
20
replies
3.0k
views
11 follow
Forum: What are the most popular NGS tools?
ensembl NGS
updated 5 months ago by 40k • written 7.4 years ago by 23k
7
votes
20
replies
1.6k
views
Forum: NGS RNA-Seq Analysis Pipeline Tophat vs STAR
STAR RNA-Seq TopHat
updated 4 months ago by 40k • written 2.7 years ago by ▴ 10
30
votes
19
replies
8.0k
views
6 follow
Forum: Programming language use distribution from recent programs / articles
programming-language programs
updated 4 months ago by 40k • written 6.4 years ago by 11k
35
votes
19
replies
3.3k
views
6 follow
Forum: For the general public seeking advice from this community
diagnosis rare-disease
updated 12 months ago by 40k • written 8.0 years ago by 11k
35
votes
19
replies
3.6k
views
Forum: Crowd Sourcing The 'Analysis' Of The 'Big Foot' Genome
bigfoot genome
updated 7 months ago by 40k • written 10.6 years ago by 4.5k
47
votes
19
replies
13k
views
10 follow
Forum: Is Software Development a key part of Bioinformatics?
Software-Development
updated 13 months ago by 40k • written 8.7 years ago by ▴ 70
45
votes
19
replies
2.4k
views
9 follow
Forum: Where and how NGS techniques are heading for the next 5 years?
next-gen NGS
updated 4 months ago by 40k • written 6.3 years ago by 5.8k
49
votes
19
replies
6.7k
views
13 follow
Forum: Why Are There No Proteomics Questions In Biostar?
proteomics biostars
updated 7 months ago by 40k • written 12.9 years ago by ▴ 410
57
votes
19
replies
27k
views
6 follow
Forum: Attention: Bowtie2 And Multiple Hits
next-gen bowtie mapping
updated 7 months ago by 40k • written 10.9 years ago by 10k
27
votes
19
replies
4.1k
views
10 follow
Forum: Google genomics cloud platform ?
genome cloud
updated 6 months ago by 40k • written 8.3 years ago by 12k
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 40k • written 10.6 years ago by 98k
56
votes
19
replies
3.7k
views
9 follow
Forum: How to apply for a job
resume cover-letter application CV
updated 4 months ago by 40k • written 6.2 years ago by 23k
9
votes
19
replies
8.2k
views
Forum: Careful!! Velvet Generates Different Assemblies From The Same Input Data And Same Input Parameters With Openmp Enabled.
velvet genome
updated 6 months ago by 40k • written 9.8 years ago by ▴ 650
70
votes
19
replies
5.0k
views
13 follow
Forum: Thrown Into A Bioinformatics Position
computational-analysis
updated 14 months ago by 40k • written 8.0 years ago by ▴ 170
34
votes
19
replies
7.4k
views
12 follow
Forum: Programming Language In Bioinformatics
perl python
updated 7 months ago by 40k • written 10.4 years ago by ▴ 260
38
votes
19
replies
9.8k
views
10 follow
Forum: Kallisto New RNA-seq quantification method discussion
RNA-Seq
updated 5 months ago by 40k • written 7.4 years ago by ▴ 550
21
votes
18
replies
1.4k
views
Forum: Is it safe to keep our data in github
github
updated 3 months ago by 40k • written 3.4 years ago by ▴ 70
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 40k • written 10.0 years ago by ★ 1.1k
29
votes
18
replies
2.2k
views
12 follow
Forum: what are the big questions in bioinformatics field nowadays
genome
updated 3 months ago by 40k • written 3.6 years ago by ▴ 20
72
votes
18
replies
7.0k
views
17 follow
Forum: What Is One Book Every Bioinformatician Should Read?
books
updated 6 months ago by 40k • written 10.2 years ago by 7.9k
36
votes
18
replies
7.6k
views
Forum: How Does Genomebrowse Free Genome Browser From Golden Helix Compare?
visualization genome-browser
updated 2.4 years ago by 20 • written 10.5 years ago by ▴ 140
13
votes
18
replies
2.9k
views
6 follow
Forum: Bioinformatics independent study group
Proteomic RNA-Seq Genomic
updated 4 months ago by 40k • written 6.1 years ago by ★ 1.2k
29
votes
18
replies
2.9k
views
7 follow
Forum: Should I quit PhD program?
education career research phd
updated 4 months ago by 40k • written 5.4 years ago by ▴ 30
23
votes
18
replies
1.2k
views
Forum: Versioning of Blast DB and Reproducible Research
database blast reproducible-research
updated 3 months ago by 40k • written 3.3 years ago by ▴ 50
38
votes
18
replies
3.8k
views
11 follow
Forum: Should We Have A Biostar Conference Or Meeting?
conference biostars
updated 7 months ago by 40k • written 10.3 years ago by 53k
23
votes
18
replies
2.3k
views
9 follow
Forum: How to imagine the future of bioinformatics?
bioinformatics
updated 5 months ago by 40k • written 7.0 years ago by ▴ 570
15
votes
17
replies
2.9k
views
10 follow
Forum: What does a recruiter expect from a Bioinformatician ?
expectations recruitment skills
updated 15 months ago by 40k • written 5.6 years ago by ▴ 960
13
votes
17
replies
4.5k
views
8 follow
Forum: A Universal/Common Biorep System
reputation
updated 6 months ago by 40k • written 9.8 years ago by 20k
21
votes
17
replies
8.4k
views
7 follow
Forum: In YOUR personal opinion, who are the top 5 bioinformatics researchers in NGS in 21st century?
next-gen
updated 5 months ago by 40k • written 6.7 years ago by ▴ 10
20
votes
17
replies
3.4k
views
Forum: Biostar Ads Are Here! Showcase Your Accomplishments To The World!
biostars
updated 7 months ago by 40k • written 10.3 years ago by 98k
9
votes
17
replies
2.6k
views
Forum: “Systematic pattern of excess success"
paper statistics
updated 6 months ago by 40k • written 8.8 years ago by 3.5k
13
votes
17
replies
3.6k
views
6 follow
Forum: Advice for undergraduate bioinformatics learners
advice
updated 13 months ago by 40k • written 7.8 years ago by ▴ 10
41
votes
17
replies
37k
views
15 follow
Forum: List Of Genome Sequencing Centers/Institutes
genomics institutes
updated 7 months ago by 40k • written 10.6 years ago by 19k
33
votes
17
replies
3.0k
views
7 follow
Forum: What bioinformatics tools/software do not get enough recognition?
software
updated 6 months ago by 40k • written 8.9 years ago by 24k
1,000 results • Page 3 of 20
Recent Votes
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti
Comment: Error in bowtie2
Recommended Tools For Alternative Splicing Detection From Rna-Seq Data
Comment: Using STAR aligner to build index of hg38
Answer: How to sort using samtools
The Biostar Handbook. A bioinformatics e-book for beginners.
The Biostar Handbook. A bioinformatics e-book for beginners.
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Recent Replies
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti by Y • 0
I tried the commands you recommended in the bash/command line. When I tried `find "${bam_directory}" -type f -name "*.bam" | xargs samtools…
Comment: Hugo_Symbol to Entrez ID by GenoMax 134k
Can you provide some examples of HUGO ID's you are unable to convert?
Comment: Using STAR aligner to build index of hg38 by GenoMax 134k
GTF file includes gene models/annotation information. You could also use a program like `salmon/kallisto` with just human transcriptome to…
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti by Pierre Lindenbaum 157k
then test each files. find "${bam_directory}" -type f -name "*.bam" | xargs samtools quickcheck file "${reference_gen…
Answer: Ties in reranked list by alserg ▴ 840
The problem here is not the ties, but that your gene IDs in the pathway list (ensemble human genes) does not match the names of the stats v…
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti by Y • 0
I did not use the space between the `-u` flag and the `-o` flag (the blank line) but I did do what you recommended: # Run CuffDiff wit…
Answer: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti by Pierre Lindenbaum 157k
how about simply trying: ``` cuffdiff -u "${annotation_gtf}" \ -o "${output_directory}" \ -b "${reference_genome}" \ -p "${num_th…
Comment: Using STAR aligner to build index of hg38 by Grace • 0
Yes, I know also need a GTF file. So the GTF file will include RNA information? Thanks for your answer!!
Comment: STAR Intron Motif Script Gives Segmentation fault Error by Y • 0
I will try and figure it out on my own given what you all have mentioned. Thank you for your time.
Comment: Using STAR aligner to build index of hg38 by Amitm ★ 2.2k
Have you gone through the manual [here][1]. In addition to the genome fasta file, you would also need a GTF file (of gene annotations) to b…
Comment: Highly inflated p-values in GWAS by regenie by 4galaxy77 2.8k
You still definitely need to include principle components as covariates, even if your data is from the same ethnicity. Not including those …
Answer: How to create structural variants ground truth for alignment of two long-read ge by Christophe • 0
Hi, D-genies is using minimap2 to align both genomes and minimap2 is chaining local alignments to produce a global one. If the SV are sm…
Comment: Ties in reranked list by Hamza • 0
In this case there are no results in my fgsea object unfortunately
Comment: Genes with promoter and enhancer regions as GTF by abis.1819104 • 0
how to generate promoters.bed and enhancer.bed files from gtf file
Comment: Deepvariant variant calling by singularity by jeffhsu3 • 0
I am having a similar issue was this ever resolved? Getting this error: I0922 22:22:08.794076 140356687390528 make_examples_core.py:257] O…
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