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460 results • Page 2 of 10
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3
votes
3
replies
905
views
Forum: Importance of Data Structures for Bioinformatics?
data-structures
updated 7 months ago by 43k • written 7 months ago by • 0
19
votes
14
replies
2.1k
views
Forum: What is the amount of sequencing data produced annually?
data research sequencing
updated 7 months ago by 22k • written 7 months ago by ▴ 70
19
votes
10
replies
1.5k
views
Forum: Pain points using commercial clouds
gpt tinybio
updated 7 months ago by ▴ 70 • written 7 months ago by ▴ 840
9
votes
6
replies
1.9k
views
6 follow
Forum: GTF files from Ensembl Releases 105 and 106 unsorted
Ensembl bug GTF
updated 7 months ago by 82k • written 17 months ago by ▴ 30
3
votes
2
replies
619
views
Forum: How to contribute to the next edition of Biostars Handbook
handbook
updated 7 months ago by 43k • written 7 months ago by ▴ 20
3
votes
6
replies
1.4k
views
6 follow
Forum: Is Bioinformatics a Professional Degree?
career degree
7 months ago by anasjamshed ▴ 120
2
votes
5
replies
948
views
6 follow
Forum: Biostar as a next generation version
meta mobile-app
updated 6 months ago by 43k • written 7 months ago by • 0
2
votes
9
replies
1.2k
views
Forum: open source projects looking for contributors
open-source
updated 7 months ago by ▴ 70 • written 7 months ago by ▴ 20
0
votes
0
replies
535
views
Forum: Recruiters: what do you expect on a junior bioinformatician?
career skills
updated 8 months ago by 43k • written 8 months ago by ▴ 20
3
votes
4
replies
1.4k
views
Forum: Discussion: Uploading terabytes of data to NCBI SRA
NCBI WGS archiving servers remote
updated 8 months ago by 141k • written 8 months ago by ▴ 130
0
votes
0
replies
566
views
Forum: I have a Master's and little experience in Bioinformatics - what would be the next best step?
career
updated 8 months ago by 43k • written 8 months ago by ▴ 10
1
vote
3
replies
771
views
Forum: Spaceranger missing spatial coordinates [Discussion]
Visium
updated 8 months ago by 141k • written 8 months ago by ▴ 550
11
votes
8
replies
1.4k
views
6 follow
Forum: How to write a review article in bioinformatics
article review
updated 7 months ago by 43k • written 8 months ago by ▴ 10
364
votes
58
replies
69k
views
44 follow
Forum: Recommend Your Favorite Bioinformatics Books
education books
updated 6 months ago by 43k • written 14.1 years ago by 100k
1
vote
2
replies
18k
views
Forum: Would you rather analyze a dataset with a strong, non-collinear batch effect, or a weak, collinear batch effect.
collinear latent batch-effect variable GLM
9 months ago by LauferVA 4.2k
0
votes
3
replies
3.8k
views
10 follow
Forum: Discussion question: Cutoff for SNP phylogeny
Phylogenetics SNP
written 17 months ago by ▴ 120
2
votes
3
replies
786
views
Forum: Purely analytic or in silico manuscripts that have significantly improved biological understanding
dry-lab
updated 9 months ago by 141k • written 9 months ago by 4.2k
0
votes
2
replies
1.3k
views
Forum: [Detailed Question] How to Normalize of Metagenomics Gene Abundances (with HMMs models)
normalization
updated 10 months ago by 10k • written 10 months ago by • 0
33
votes
23
replies
4.1k
views
8 follow
Forum: Is there a file format better suited for the era of pangenomics than the .vcf? What are its attributes?
VCF file-format genomics
updated 10 months ago by 22k • written 10 months ago by 4.2k
7
votes
8
replies
1.9k
views
Forum: Would solving many Rosalind problems show your ability for this field in job-wise?
rosalind career
10 months ago by K • 0
2
votes
3
replies
859
views
Forum: Mapping a predicted sequence to a genome
predicted map alignment sequence
updated 10 months ago by ★ 27k • written 10 months ago by • 0
0
votes
0
replies
441
views
Forum: Recommendation sought for differential exon usage of a single gene
splicing differential-exon-usage
updated 10 months ago by 43k • written 10 months ago by ▴ 10
7
votes
4
replies
1.1k
views
Forum: [Meta] Use of AI
AI Artificial-Intelligence meta ChatGPT
updated 10 months ago by 43k • written 10 months ago by 4.2k
2
votes
2
replies
596
views
Forum: Colleges
Colleges india universities
updated 10 months ago by 43k • written 10 months ago by • 0
19
votes
15
replies
2.0k
views
6 follow
Forum: Cross out line in Biostars
meta
updated 11 months ago by 43k • written 5.9 years ago by 5.3k
121
votes
33
replies
39k
views
24 follow
Forum: Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 11 months ago by ★ 2.5k • written 10.7 years ago by 11k
103
votes
42
replies
31k
views
34 follow
Forum: List of cloud genomics companies
cloud-genomics
updated 16 days ago by 22k • written 10.4 years ago by ★ 3.6k
26
votes
12
replies
7.5k
views
6 follow
Forum: Mapping God Found ‘Scientifically Dishonest’ By Anonymous Peer Reviewers
ngs
updated 11 months ago by ▴ 10 • written 10.5 years ago by ▴ 50
0
votes
2
replies
765
views
Forum: How to start in bioinformatics?
career
updated 11 months ago by 43k • written 12 months ago by • 0
4
votes
5
replies
1.4k
views
Forum: I'm looking for a mentor in Bioinformatics
mentor teaching
updated 10 weeks ago by • 0 • written 12 months ago by • 0
10
votes
15
replies
2.1k
views
Forum: How should reference genome fasta files be distributed by UCSC?
reference-genome fasta freeze ucsc-genome-browser
updated 10 months ago by 22k • written 14 months ago by ★ 1.6k
5
votes
4
replies
1.3k
views
Forum: Best BAM viewer in 2022
sam bam
updated 10 months ago by 43k • written 17 months ago by ▴ 70
1.2k
votes
206
replies
59k
views
108 follow
Forum: What Are The Most Common Stupid Mistakes In Bioinformatics?
software
updated 10 months ago by ★ 1.4k • written 13.1 years ago by 22k
15
votes
13
replies
4.1k
views
8 follow
Forum: Does a PhD or work experience set you up better to do bioinformatics work in industry?
advice industry phd
updated 3 months ago by 3.9k • written 17 months ago by ▴ 30
4
votes
5
replies
1.4k
views
6 follow
Forum: Which Bioinformatics Master's degree is better?
career masters
updated 11 months ago by 43k • written 18 months ago by • 0
3
votes
6
replies
1.1k
views
Forum: How to become a moderator and other ways of contributing to Biostars
meta biostars
updated 11 months ago by 43k • written 18 months ago by 6.2k
3
votes
2
replies
845
views
Forum: From protein-protein interaction networks to..
workflow computational knowledge limitations
updated 10 months ago by 43k • written 22 months ago by ▴ 50
15
votes
11
replies
4.7k
views
9 follow
Forum: Methodological problems are extremely common for enrichment analysis - beware the pitfalls before you publish
GSEA DAVID enrichment-analysis -geneontology
updated 11 months ago by 43k • written 2.1 years ago by ★ 1.9k
0
votes
3
replies
923
views
Forum: Project Topics on bioinformatic
Data-analysis Coding Molecular-biology
updated 11 months ago by 43k • written 2.2 years ago by • 0
3
votes
1
reply
908
views
Forum: How to download multiple .gz files from Ensembl Protists database
wget protist ensembl
updated 9 weeks ago by ★ 1.7k • written 2.2 years ago by ▴ 840
17
votes
14
replies
3.3k
views
Forum: Asking for feedback on a Python library for computing alignments
alignment Python
updated 10 months ago by ▴ 220 • written 2.3 years ago by ▴ 60
0
votes
1
reply
766
views
Forum: What are the most important papers/methods in Genomics/Bioinformatics of 2021?
publications
updated 10 months ago by 43k • written 2.3 years ago by ★ 2.5k
12
votes
7
replies
7.0k
views
Forum: Differences between SMART-seq2, SMART-seq3, and 10x
cell smartseq UMIs single 10x
updated 4 weeks ago by ★ 5.8k • written 2.6 years ago by ▴ 70
0
votes
0
replies
516
views
Forum: Poll about a structured description of a tool, a pipeline
survey pipeline
updated 10 months ago by 43k • written 2.7 years ago by • 0
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
11
votes
9
replies
2.4k
views
7 follow
Forum: Feature Selection and Dimensionality Reduction in 10X scRNA-seq data
software-error pca scRNA-seq
updated 11 months ago by 43k • written 4.3 years ago by 82k
0
votes
0
replies
696
views
Forum: where to get the site mutation rate of SARS-CoV-2?
sequence sequencing
updated 11 months ago by 43k • written 3.3 years ago by ▴ 40
6
votes
5
replies
1.6k
views
Forum: Very generally speaking, what are valid criteria to decide that a sample is an outlier?
outliers
updated 11 months ago by 43k • written 3.3 years ago by ▴ 300
7
votes
4
replies
1.2k
views
Forum: Specific question on torturing the data until it confesses
ipa gene-set-enrichment statistics
updated 11 months ago by 43k • written 3.3 years ago by ▴ 300
7
votes
3
replies
1.3k
views
Forum: Is it still recommended to avoid macOS Big Sur?
mac
updated 11 months ago by 43k • written 3.3 years ago by ▴ 210
460 results • Page 2 of 10
Recent Votes
Comment: downloading genomes in fasta format from accession ids
Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
Comment: To get p-values for the TPM
A: Where To Download Pam50 Gene Set?
A: Where To Download Pam50 Gene Set?
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Recent Replies
Comment: Adding CB tag to bam file by swbarnes2 14k
I think both these programs are just adding the same tag to every line. I don't think either cares whether it's called RG or CB
Comment: PCA plot (Suggestions Needed) by swbarnes2 14k
Even if this was real data, the tiny numbers for the PC1 and PC2 indicate that the differences between the samples are all absolutely tiny.…
Comment: Creating Synthetic Sequences for a ML Model by biochugs • 0
Thanks for the input. I'll continue to think of more ideas that may be achievable.
Comment: PCA plot (Suggestions Needed) by Jeremy ▴ 890
You could also try kernel PCA, which is a non-linear form of PCA, although this will be more time-consuming.
Comment: Troubleshooting RNA-seq data with DNA contamination by DKA ▴ 40
I have unstranded RNA-seq data. Please share the tool with me, if you do not mind.
Comment: PCA plot (Suggestions Needed) by Mensur Dlakic ★ 27k
Everything that @f1f58aed said, plus that there may be no data manipulation that will give you the clusters you expected. Sometimes there a…
Answer: Creating Synthetic Sequences for a ML Model by Mensur Dlakic ★ 27k
It is a good idea, though I don't see how it would work in practice. I think you will encounter at least additional problem on top of da…
Answer: PCA plot (Suggestions Needed) by Jeremy ▴ 890
Right now, the WT samples are clustering together, but you have one mutant sample off by itself, which could be an outlier. How did you sc…
Comment: Adding CB tag to bam file by GenoMax 141k
@yokofakun had written this: https://www.biostars.org/p/336965/ https://github.com/ruqianl/appendCB may also be useful.
Comment: Troubleshooting RNA-seq data with DNA contamination by GenoMax 141k
Please post information about your tool as a `tools` category post. Don't wait/ask other users to ask you.
Comment: Adding CB tag to bam file by Maria • 0
Sorry for the delay in my answer, I got sidetracked. I am using ```samtools addreplacerg -r "@RG\tID:$cell" -o $cell.bam -h $LINE``` bu…
Answer: Troubleshooting RNA-seq data with DNA contamination by haibol2017 ▴ 10
We just developed a R package to tackle this problem. Do you have stranded or unstranded RNA-seq data contaminated with gDNA? If you wou…
Comment: How to trim transcripts using information from NCBI contamination screen report by GenoMax 141k
`bbduk.sh` can use the transcripts as input. There is a `adapters.fa` included in the `resources` directory of the distribution. You can do…
Comment: PCA plot (Suggestions Needed) by swbarnes2 14k
Cross posted here (including the code used to make up the counts): https://support.bioconductor.org/p/9157911/#9157959
Comment: To get p-values for the TPM by swbarnes2 14k
RSEM returns a kind of p-value if you run it with the "prior-enhanced" option. Did you do that? Are you completely sure that's the value y…
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