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161
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22
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18k
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19 follow
Forum: Advice For Newcomers To The Bioinformatics Field
advice career
updated 18 months ago by 43k • written 10.8 years ago by 9.7k
84
votes
22
replies
4.6k
views
12 follow
Forum: is fortran still used in bioinformatics?
FORTRAN R
updated 14 months ago by 43k • written 4.9 years ago by ▴ 190
99
votes
21
replies
9.0k
views
14 follow
Forum: How Has Bioinformatics Improved Over Time?
bioinformatics
updated 14 months ago by 43k • written 11.3 years ago by ▴ 370
39
votes
21
replies
14k
views
10 follow
Forum: Orientation of PE reads a review of --fr --ff and --rf meanings
RNA-Seq
updated 11 months ago by 43k • written 5.6 years ago by 8.6k
42
votes
21
replies
15k
views
10 follow
Forum: A Database Of Signatures Of Selection In The 1000 Genomes Dataset
1000genomes human selection
updated 14 months ago by 43k • written 10.2 years ago by 28k
17
votes
21
replies
3.5k
views
8 follow
Forum: bioinformatics thesis
thesis
updated 3.0 years ago by 21k • written 3.1 years ago by ▴ 40
66
votes
21
replies
6.8k
views
18 follow
Forum: Is there anyone who was a pure biologist?
next-gen
updated 14 months ago by 43k • written 10.0 years ago by ▴ 100
35
votes
21
replies
3.1k
views
11 follow
Forum: Should you restrict use of your software based on your political views?
software
updated 20 months ago by 43k • written 8.6 years ago by 27k
29
votes
21
replies
6.3k
views
Forum: PhD vs Field application scientist in industry
career
updated 13 months ago by 43k • written 7.7 years ago by ▴ 80
81
votes
21
replies
5.1k
views
16 follow
Forum: [UPDATE] Thrown into a Bioinformatics Position
bioinformatics
updated 13 months ago by 43k • written 7.9 years ago by ★ 3.2k
67
votes
21
replies
6.1k
views
8 follow
Forum: Meta: Markdown in Biostars (now enabled)
meta
13 months ago by Ram 43k
27
votes
21
replies
9.3k
views
9 follow
Forum: Better for my career: Degree in computer science or Phd in bioinformatics?
computer-science phd
updated 13 months ago by 43k • written 7.6 years ago by ★ 1.7k
36
votes
21
replies
19k
views
9 follow
Forum: What Is Your Favorite Conserved Protein?
protein conservation
updated 14 months ago by 43k • written 10.7 years ago by 11k
20
votes
21
replies
2.9k
views
6 follow
Forum: Next Gen seq for Job interview
next-gen
updated 13 months ago by 43k • written 9.2 years ago by ▴ 20
7
votes
20
replies
2.1k
views
Forum: NGS RNA-Seq Analysis Pipeline Tophat vs STAR
STAR RNA-Seq TopHat
updated 11 months ago by 43k • written 3.3 years ago by ▴ 10
91
votes
20
replies
20k
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 19 months ago by 43k • written 10.0 years ago by 20k
42
votes
20
replies
3.4k
views
11 follow
Forum: What are the most popular NGS tools?
ensembl NGS
updated 13 months ago by 43k • written 8.1 years ago by 23k
50
votes
20
replies
6.0k
views
18 follow
Forum: Explain bioinformatics to a 10 year old
bioinformatics
updated 14 months ago by 43k • written 8.2 years ago by ★ 1.1k
49
votes
20
replies
2.1k
views
10 follow
Forum: First experiences matter
first-time tolerance
updated 3 months ago by ★ 2.6k • written 4 months ago by ★ 27k
12
votes
20
replies
3.3k
views
Forum: Starting a career in Bioinformatics
career
updated 13 months ago by 43k • written 7.9 years ago by ▴ 10
56
votes
19
replies
4.1k
views
9 follow
Forum: How to apply for a job
resume cover-letter application CV
updated 11 months ago by 43k • written 6.8 years ago by 23k
70
votes
19
replies
5.6k
views
13 follow
Forum: Thrown Into A Bioinformatics Position
computational-analysis
updated 22 months ago by 43k • written 8.6 years ago by ▴ 170
47
votes
19
replies
14k
views
10 follow
Forum: Is Software Development a key part of Bioinformatics?
Software-Development
updated 20 months ago by 43k • written 9.3 years ago by ▴ 70
50
votes
19
replies
4.9k
views
7 follow
Forum: Proposal: Biostar Wants To Run Your Ads. Feedback Requested.
biostars
updated 14 months ago by 43k • written 11.2 years ago by 100k
9
votes
19
replies
8.6k
views
Forum: Careful!! Velvet Generates Different Assemblies From The Same Input Data And Same Input Parameters With Openmp Enabled.
velvet genome
updated 14 months ago by 43k • written 10.5 years ago by ▴ 660
45
votes
19
replies
2.9k
views
9 follow
Forum: Where and how NGS techniques are heading for the next 5 years?
next-gen NGS
updated 12 months ago by 43k • written 6.9 years ago by 5.8k
35
votes
19
replies
3.8k
views
6 follow
Forum: For the general public seeking advice from this community
diagnosis rare-disease
updated 20 months ago by 43k • written 8.6 years ago by 11k
57
votes
19
replies
28k
views
6 follow
Forum: Attention: Bowtie2 And Multiple Hits
next-gen bowtie mapping
updated 14 months ago by 43k • written 11.6 years ago by 11k
30
votes
19
replies
10k
views
6 follow
Forum: Programming language use distribution from recent programs / articles
programming-language programs
updated 12 months ago by 43k • written 7.0 years ago by 11k
27
votes
19
replies
4.6k
views
10 follow
Forum: Google genomics cloud platform ?
genome cloud
updated 13 months ago by 43k • written 8.9 years ago by 12k
34
votes
19
replies
7.9k
views
12 follow
Forum: Programming Language In Bioinformatics
perl python
updated 14 months ago by 43k • written 11.0 years ago by ▴ 260
38
votes
19
replies
10k
views
10 follow
Forum: Kallisto New RNA-seq quantification method discussion
RNA-Seq
updated 13 months ago by 43k • written 8.1 years ago by ▴ 550
35
votes
19
replies
4.0k
views
Forum: Crowd Sourcing The 'Analysis' Of The 'Big Foot' Genome
bigfoot genome
updated 14 months ago by 43k • written 11.2 years ago by 4.5k
49
votes
19
replies
7.3k
views
13 follow
Forum: Why Are There No Proteomics Questions In Biostar?
proteomics biostars
updated 14 months ago by 43k • written 13.5 years ago by ▴ 410
23
votes
18
replies
2.6k
views
9 follow
Forum: How to imagine the future of bioinformatics?
bioinformatics
updated 13 months ago by 43k • written 7.6 years ago by ▴ 570
29
votes
18
replies
2.7k
views
12 follow
Forum: what are the big questions in bioinformatics field nowadays
genome
updated 11 months ago by 43k • written 4.2 years ago by ▴ 20
38
votes
18
replies
4.2k
views
11 follow
Forum: Should We Have A Biostar Conference Or Meeting?
conference biostars
updated 14 months ago by 43k • written 10.9 years ago by 54k
29
votes
18
replies
3.3k
views
7 follow
Forum: Should I quit PhD program?
education career research phd
updated 11 months ago by 43k • written 6.0 years ago by ▴ 30
13
votes
18
replies
3.2k
views
6 follow
Forum: Bioinformatics independent study group
Proteomic RNA-Seq Genomic
updated 11 months ago by 43k • written 6.7 years ago by ★ 1.3k
36
votes
18
replies
8.2k
views
Forum: How Does Genomebrowse Free Genome Browser From Golden Helix Compare?
visualization genome-browser
updated 3.1 years ago by 20 • written 11.1 years ago by ▴ 140
72
votes
18
replies
7.5k
views
17 follow
Forum: What Is One Book Every Bioinformatician Should Read?
books
updated 14 months ago by 43k • written 10.9 years ago by 8.4k
21
votes
18
replies
1.8k
views
Forum: Is it safe to keep our data in github
github
updated 11 months ago by 43k • written 4.0 years ago by ▴ 70
52
votes
18
replies
6.3k
views
14 follow
Forum: Do You Feel Good Or Bad About Putting Your Photo At Biostar?
meta biostars
updated 14 months ago by 43k • written 10.7 years ago by ★ 1.1k
23
votes
18
replies
1.5k
views
Forum: Versioning of Blast DB and Reproducible Research
database blast reproducible-research
updated 11 months ago by 43k • written 4.0 years ago by ▴ 60
42
votes
17
replies
38k
views
15 follow
Forum: List Of Genome Sequencing Centers/Institutes
genomics institutes
updated 14 months ago by 43k • written 11.2 years ago by 19k
27
votes
17
replies
5.1k
views
Forum: Data sharing via Bittorrent is coming to Biostar
biostars bittorrent
updated 14 months ago by 43k • written 9.8 years ago by 100k
9
votes
17
replies
3.0k
views
Forum: “Systematic pattern of excess success"
paper statistics
updated 14 months ago by 43k • written 9.4 years ago by 3.5k
38
votes
17
replies
3.2k
views
7 follow
Forum: Why does bioinformatics use a special format like a BAM file instead of a database like SQLite?
sam bam samtools
updated 10 months ago by 43k • written 3.7 years ago by ▴ 250
15
votes
17
replies
3.3k
views
10 follow
Forum: What does a recruiter expect from a Bioinformatician ?
expectations recruitment skills
updated 22 months ago by 43k • written 6.2 years ago by ▴ 960
29
votes
17
replies
2.3k
views
6 follow
Forum: Can Biostars use question template like Github issue/PR?
meta biostars template
updated 12 months ago by 43k • written 7.2 years ago by 8.5k
1,000 results • Page 3 of 20
Recent Votes
Answer: MSA and distance matrix in R
Comment: MSA and distance matrix in R
Comment: Which hg38 file?
Answer: Which hg38 file?
Answer: Where to get the following bed file?
How to save GRanges object to csv file
Answer: How to get proteins from GFF file resulted from MAKER annotation
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Recent Replies
Comment: We created a Bioinformatics Competition for Spatial Transcriptomics: MICOS-EU by MICOS • 0
Contest question details: **To effectively address the accuracy and efficiency issues of clustering algorithms used for spatial transcript…
Comment: HCL database download by sooni ▴ 20
I would like to download top markers for each subpopulation data. Is there no way? It seems different from the DGE data.
Comment: Understanding STAR output (Aligned.out.sam file) by GenoMax 142k
Refer to SAM alignment format: https://samtools.github.io/hts-specs/SAMv1.pdf Check section 1.4.
Answer: Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genom by LChart 3.9k
Step 1: Go to TCGA in the GDC and open the Cohort Builder https://portal.gdc.cancer.gov/analysis_page?app=CohortBuilder&tab=general Step …
Comment: Where to get the following bed file? by GenoMax 142k
SeqCap kits are discontinued. If you don't find the said file your will need to email Roche Support per this page: https://sequencing.roche…
Answer: Where to get the following bed file? by LChart 3.9k
UCSC maintains a list of exome probe sets and targets. You could check there: https://hgdownload.soe.ucsc.edu/gbdb/hg19/exomeProbesets/
Comment: How to compute TPM normalized values for TCGA miRNA data? by Ngrin • 0
Yes, I found some similar ideas on biostar repository. So you think the authors have done something wrong? And I should only consider CPM?
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA by Chris Dean ▴ 390
It is difficult to answer how they were able to identify *S. hominis* without seeing the code or paper. To address your second question, i…
Comment: Problem with Seurat package in PercentageFeatureSet function by bk11 ★ 2.4k
Did you check where the `features.tsv.gz` file had Gene IDs or Ensembl IDs?
Answer: How to compute TPM normalized values for TCGA miRNA data? by dsull ★ 6.0k
TPM is irrelevant for miRNA-seq; CPM works fine. TPM tries to adjust for length effects by dividing by gene length (e.g. reducing the im…
Comment: Applying the metacell2 algorithm using python by Wayne ★ 2.0k
"I'm also unsure what qualifies as a lateral gene." The [README where you reference](https://metacells.readthedocs.io/en/latest/readme.htm…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA by sovrappensiero ▴ 90
Ah, yes this makes sense! I knew this was an issue with, say, using kraken2 on shotgun metagenomic reads, but I don't have a lot of experi…
Comment: How to access TCGA samples that were treated with a specific drug? by Qroid ▴ 40
Thank you. Maybe it's best to confirm with the authors about how they're getting responder/non-responder labels. I'll do that now.
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA by Chris Dean ▴ 390
If you sequenced a short hypervariable region, most of your sequence reads will not be able to be assigned to the species level. One possi…
Comment: anRichment is missing by GenoMax 142k
Consider emailing Dr. Horvath about this. Until enough people make him aware of this issue WGCNA "problem" is unlikely to get fixed.
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