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21,181 results • Page 3 of 424
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82
votes
19
replies
12k
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8 follow
Future Directions In Bioinformatics
subjective career
updated 7 months ago by 40k • written 12.8 years ago by ★ 1.5k
81
votes
8
replies
8.1k
views
6 follow
Tutorial: Current Topics in Genome Analysis 2014 (collection of educational lectures)
workshop lectures genomics training
updated 6 months ago by 40k • written 9.3 years ago by 19k
81
votes
39
replies
6.6k
views
11 follow
News: State Of Biostar - Future Directions (January 2013)
biostars
updated 7 months ago by 40k • written 10.7 years ago by 98k
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
81
votes
21
replies
40k
views
15 follow
How To Get Bed File Containing Exons Of Canonical Transcripts And Their Corresponding Gene Symbols
bed transcript ucsc biomart
updated 6 days ago by ▴ 180 • written 9.6 years ago by ▴ 750
80
votes
34
replies
4.4k
views
11 follow
Forum: Authorship issues- how to resolve?
authorship
updated 8 months ago by 40k • written 8.3 years ago by ▴ 520
80
votes
23
replies
4.7k
views
11 follow
Forum: Are we facing a bioinformatician shortage?
salary career
updated 6 months ago by 40k • written 8.9 years ago by ★ 3.0k
79
votes
22
replies
86k
views
16 follow
How To Split One Big Sequence File Into Multiple Files With Less Than 1000 Sequences In A Single File
next-gen sequencing fasta rna r perl
updated 10 months ago by 40k • written 11.9 years ago by ▴ 290
79
votes
35
replies
8.5k
views
17 follow
Forum: Do bioinformaticians often break molecular biologists' hearts by being the first author?
authorship career
updated 3 months ago by • 0 • written 7.8 years ago by ▴ 650
78
votes
31
replies
6.1k
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
77
votes
22
replies
22k
views
14 follow
Assessing The Quality Of De Novo Assembled Data
assembly next-gen
updated 11 months ago by 40k • written 11.3 years ago by ★ 2.7k
77
votes
86
replies
27k
views
20 follow
Tool: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
clumpify storage bbmap pigz compression
updated 3 months ago by 40k • written 6.8 years ago by 18k
76
votes
70
replies
17k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
updated 6 months ago by 40k • written 5.6 years ago by 86k
76
votes
24
replies
57k
views
16 follow
How To Sort Bed Format File
bed
updated 11 months ago by 156k • written 10.6 years ago by ▴ 450
76
votes
22
replies
52k
views
17 follow
How To Download All Sra Samples At Once ?
geo sra
updated 6 months ago by 40k • written 9.6 years ago by ★ 1.5k
76
votes
35
replies
28k
views
13 follow
Illumina Instrument Type from fastq?
fastq
updated 4 months ago by ▴ 20 • written 7.2 years ago by 6.5k
75
votes
14
replies
12k
views
10 follow
Tool: karyoploteR: uncircle your genomes
karyoploteR Rdataviz NGS
updated 3 months ago by 40k • written 6.3 years ago by ★ 3.4k
75
votes
18
replies
1.9k
views
11 follow
Blog: A list of technical advantages of Snakemake over Nextflow | Cloud solution for Snakemake
Snakemake
updated 2 days ago by 40k • written 6 days ago by ▴ 30
75
votes
13
replies
66k
views
10 follow
Tutorial: Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r cancer classification
updated 10 months ago by 40k • written 9.8 years ago by ★ 1.2k
75
votes
14
replies
15k
views
15 follow
Tutorial: List Of Bioinformatics Books
books
updated 7 months ago by 40k • written 10.3 years ago by 9.7k
74
votes
16
replies
4.3k
views
10 follow
Tools & Techniques Bioinformatician Have To Master?
subjective
updated 12 weeks ago by 40k • written 12.5 years ago by ★ 3.3k
74
votes
15
replies
35k
views
8 follow
About Paired-End Sequencing
next-gen-sequencing duplicates
updated 12 weeks ago by 40k • written 13.4 years ago by 156k
74
votes
20
replies
34k
views
16 follow
How to know that your RNA-seq is stranded or not?
RNA-Seq
updated 10 weeks ago by ▴ 80 • written 9.4 years ago by ▴ 620
73
votes
60
replies
25k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 7 months ago by 40k • written 6.0 years ago by 86k
73
votes
29
replies
3.7k
views
12 follow
Tool: ChatGPT optimized for bioinformatics questions
gpt
10 weeks ago by Sasha ▴ 720
72
votes
14
replies
3.7k
views
12 follow
Forum: Things you wish you knew when entering the bioinformatics field
pitfalls advice
updated 3 months ago by 40k • written 3.0 years ago by ★ 15k
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
72
votes
20
replies
25k
views
11 follow
Parsing Ncbi Taxonomic Tree?
ncbi taxonomy python tree
updated 9 months ago by 40k • written 11.9 years ago by ▴ 350
72
votes
71
replies
27k
views
17 follow
Tool: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling
volcano-plot bioconductor ggplot2 ggrepel
updated 3 months ago by 40k • written 5.1 years ago by 86k
72
votes
48
replies
16k
views
15 follow
Tutorial: For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs alignment bwa
updated 6 months ago by 40k • written 10.6 years ago by 33k
72
votes
20
replies
83k
views
15 follow
How To Get Ensembl Id (Gene, Transcript, Protein) Mapping Information?
ensembl identifiers mapping
updated 8 months ago by 40k • written 12.9 years ago by ▴ 180
72
votes
48
replies
7.6k
views
18 follow
What Kind Of Bioinformatics Tutorials Would You Like To See Online?
education
updated 7 months ago by 40k • written 12.4 years ago by 13k
71
votes
26
replies
26k
views
15 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 6 months ago by 40k • written 9.6 years ago by 98k
70
votes
16
replies
9.4k
views
11 follow
Creating A New Bioinformatics Unit
core career
updated 7 months ago by 40k • written 12.2 years ago by ▴ 790
69
votes
25
replies
6.5k
views
16 follow
How Do You Explain What You Do To The Guy On The Street Or Your Mum?
general
updated 7 months ago by 40k • written 13.5 years ago by ▴ 190
69
votes
39
replies
3.7k
views
14 follow
Forum: Preparation for Bioinformatics.SE closing
meta biostars
updated 4 months ago by 40k • written 6.3 years ago by 13k
69
votes
17
replies
34k
views
12 follow
Transform a GTF file into a data frame in R
R RNA-Seq GTF
updated 6 months ago by 40k • written 6.0 years ago by ▴ 410
68
votes
22
replies
7.0k
views
16 follow
Forum: Learning Python: list of resources
python
updated 5 months ago by 40k • written 6.9 years ago by ★ 2.8k
68
votes
48
replies
7.6k
views
16 follow
Forum: Stranger Things: unexpected limitations of popular tools
samtools hisat2
updated 4 months ago by 40k • written 6.2 years ago by 98k
67
votes
21
replies
5.5k
views
8 follow
Forum: Meta: Markdown in Biostars (now enabled)
meta
6 months ago by Ram 40k
67
votes
15
replies
32k
views
14 follow
Rna-Seq Pipeline
pipeline next-gen-sequencing rna rna-seq
updated 4 months ago by 40k • written 13.3 years ago by 24k
67
votes
6
replies
25k
views
7 follow
Tutorial: Rna-Seq Review Papers
RNA-seq papers
updated 7 months ago by 40k • written 11.1 years ago by 98k
66
votes
6
replies
25k
views
8 follow
What Is A "Spot" In Sra Format
sra fastq format
updated 7 months ago by 40k • written 12.0 years ago by 4.1k
66
votes
18
replies
115k
views
14 follow
from .BAM to .BAI using samtools
next-gen-sequencing samtools
updated 12 weeks ago by 40k • written 9.0 years ago by ▴ 860
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
66
votes
19
replies
48k
views
17 follow
Tool To Find Out If Fastq Is In Sanger Or Phred64 Encoding?
fastq
updated 3 months ago by 40k • written 10.6 years ago by ★ 3.6k
65
votes
10
replies
3.1k
views
6 follow
Incentive For Learning Emboss
emboss
updated 12 weeks ago by 40k • written 12.4 years ago by 11k
65
votes
3
replies
280k
views
Understanding up and down regulated genes from LOG2 foldchange or foldchange
protein gene-expression RNA-Seq
updated 6 months ago by 40k • written 9.3 years ago by ▴ 960
65
votes
26
replies
13k
views
11 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 6 months ago by 40k • written 4.5 years ago by 16k
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
21,181 results • Page 3 of 424
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C: bowtie2 piped to samtools created many samtools.tmp.bam files, how to get the si
What is the difference between norm --multiallelics -any versus --atomize?
Answer: What is the difference between norm --multiallelics -any versus --atomize?
A: How To Extract A Sequence From A Big (6Gb) Multifasta File ?
A: How to extract a sequence below a fasta header (">") from a fasta file ?
A: How to extract a sequence below a fasta header (">") from a fasta file ?
A: How To Extract A Sequence From A Big (6Gb) Multifasta File ?
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Recent Replies
Comment: Dealing with transcriptome sequences that are smaller than their respective gene by langziv ▴ 50
If it's difficult to tell from RNA-seq data, what other approaches I should use?
Comment: Dealing with transcriptome sequences that are smaller than their respective gene by langziv ▴ 50
I modified the question so that instead of genes the question refers to CDSs.
Comment: Dealing with transcriptome sequences that are smaller than their respective gene by langziv ▴ 50
Thanks. Is there an approach or a guideline to filter such sequences?
Answer: Assistance with Fungal Genome Annotation Using Maker and BLAST by Juke34 8.2k
There are tools to combine output from blast in tabulated format like in the example here [enter link description here][1](see functional …
Answer: Importance of Data Structures for Bioinformatics? by xiaoguang ▴ 120
Bioinformatics is a cross-disciplinary research subject and learning anything is a plus for future participation in related jobs. But right…
Answer: How to find positions with higher depth relative to their surroundings by xiaoguang ▴ 120
I saw you want to get regions that have significantly higher depth than their surroundings; you must get a p-value to show significant as w…
Comment: how to calculate BAF and LRR from VCF or BCF files? by xiaoguang ▴ 120
Hi, The ASCAT new version has introduced a new function called `ascat.prepareHTS`, which can be used to prepare all files that are required…
Comment: GERP++ (gerpcol) error on a test data by Diana • 0
I solved the problem in the end. I was under the impression that the reference sequence had to be provided in a separate fasta file: c…
Answer: How to find positions with higher depth relative to their surroundings by d-cameron ★ 2.9k
The usual way of doing this is to use one of the many existing copy number variant caller. Doing this yourself is both a) complicated to do…
Answer: How to retrieve LoF and missense variants in WES data? by luffy ▴ 30
@ _quantum_girl_, as Pierre mentioned, you can annotate your VCF with [snpEff][1] or [ensembl vep][2] once you annotated you could filter n…
Comment: Adding a control sample to bulk RNA-seq by Chris ▴ 180
Thank you so much! It is from the same lab but from another project. Would you please explain about combining the counts together a little …
Answer: Importance of Data Structures for Bioinformatics? by d-cameron ★ 2.9k
> how important are Data Structures to multi-omic / bioinformatic analysis Generally speaking, they're not critical if you are using an …
Answer: Recommended order of operations for identifying the genomic location and copy-nu by dk0319 ▴ 70
Update: The above workflow was successful, in that contig_1719 does contain approximately 4 copies of my insert based on searching pieces o…
Comment: manhattan plot with vcf information by sooni ▴ 10
I want to find out specific genes using the manhattan plot. I divide the patients into two groups, controls and patients, and try to identi…
Comment: Importance of Data Structures for Bioinformatics? by dsull ★ 4.6k
If you don't want to hurt your GPA, why not just take the course pass/fail or, if that's not an option, simply audit it? I doubt anyone wi…
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