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1,000 results • Page 2 of 20
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132
votes
27
replies
40k
views
14 follow
Why Are There Many Rna-Seq Hits To Intronic Regions?
rna-seq
updated 11 months ago by 38k • written 11.0 years ago by 33k
130
votes
123
replies
29k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 9 days ago by ★ 1.1k • written 4.4 years ago by 85k
129
votes
32
replies
122k
views
29 follow
Is There A Free Alternative To Ingenuity Pathway Analysis?
network pathway
updated 12 months ago by 38k • written 12.1 years ago by ▴ 530
127
votes
33
replies
53k
views
19 follow
VCF files: Change Chromosome Notation
vcf next-gen sequence
updated 5 months ago by 38k • written 8.9 years ago by ▴ 480
126
votes
44
replies
27k
views
16 follow
Forum: Trimming adapter sequences - is it necessary?
NGS adapter RNA-Seq
updated 22 days ago by 38k • written 6.5 years ago by ▴ 970
122
votes
42
replies
8.7k
views
21 follow
News: Help Make Biostar Better! Add Your Feedback, Opinions And Suggestions.
meta biostars
updated 6 weeks ago by 38k • written 10.3 years ago by 97k
121
votes
44
replies
19k
views
21 follow
What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
subjective
updated 6 weeks ago by 38k • written 12.8 years ago by 5.3k
118
votes
26
replies
33k
views
22 follow
Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
DESeq Kallisto RNASeq Salmon DESeq2
updated 21 days ago by ▴ 30 • written 7.9 years ago by ▴ 610
118
votes
53
replies
88k
views
22 follow
How to plot coverage and depth statistics of a bam file
bam coverage depth next-gen-sequencing
updated 13 days ago by • 0 • written 8.8 years ago by ▴ 330
117
votes
59
replies
29k
views
23 follow
Help a graduate student going into Bioinformatics looking for a new personal laptop. Should I get a Mac or a PC?
hardware next-gen
updated 7 weeks ago by 38k • written 7.9 years ago by ▴ 30
116
votes
66
replies
40k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 18 days ago by 38k • written 4.7 years ago by 71k
116
votes
74
replies
42k
views
40 follow
Is there a Lims that doesn't suck?
LIMS
updated 5 months ago by 127k • written 12.3 years ago by ★ 3.2k
116
votes
35
replies
7.0k
views
18 follow
Forum: Is Biostar Killing The Bioinformatics Core?
core biostars
updated 6 weeks ago by 38k • written 10.0 years ago by 21k
116
votes
31
replies
35k
views
24 follow
Forum: Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 9 months ago by 38k • written 9.6 years ago by 11k
115
votes
35
replies
36k
views
20 follow
Forum: Snakemake vs. Nextflow: strengths and weaknesses
snakemake nextflow Forum
updated 21 days ago by ▴ 30 • written 5.8 years ago by ▴ 760
112
votes
24
replies
45k
views
17 follow
Workflow Or Tutorial For Snp Calling?
snp samtools alignment next-gen sequencing
updated 7 months ago by 38k • written 11.9 years ago by ▴ 480
111
votes
25
replies
64k
views
14 follow
Is My Bam File Sorted ?
bam next-gen sequencing sort
updated 7 weeks ago by ▴ 10 • written 12.2 years ago by 153k
110
votes
37
replies
6.9k
views
13 follow
Bioinformatics Career Survey 2011/2012
career
updated 6 weeks ago by 38k • written 11.5 years ago by 153k
109
votes
56
replies
40k
views
23 follow
Gene Fusion Detection: Rna-Seq Data
rna-seq next-gen sequencing fusion
updated 6 months ago by 38k • written 10.8 years ago by ▴ 380
106
votes
45
replies
80k
views
30 follow
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta
updated 7 months ago by ▴ 20 • written 10.7 years ago by ▴ 320
106
votes
23
replies
20k
views
16 follow
Forum: How Did You Learn Good Practice In Bioinformatics/Computational Biology?
bioinformatics
updated 29 days ago by 38k • written 9.2 years ago by ▴ 580
105
votes
26
replies
38k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation domain r
updated 6 months ago by 38k • written 10.2 years ago by ▴ 810
105
votes
46
replies
11k
views
13 follow
Forum: Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
epigenetics
updated 4 weeks ago by 38k • written 9.6 years ago by ★ 1.1k
103
votes
12
replies
72k
views
7 follow
Bedtools Compare Multiple Bed Files?
bedtools intersect
updated 5 months ago by 38k • written 11.4 years ago by ★ 1.7k
102
votes
19
replies
17k
views
15 follow
How Does A Bioinformatics Scientist Document His/Her Work?
workflow
updated 5 weeks ago by 38k • written 10.8 years ago by ▴ 830
102
votes
30
replies
59k
views
25 follow
Tools To Find Gene Ontology Term Enrichment
gene enrichment tool
updated 9 months ago by 38k • written 13.1 years ago by ★ 1.0k
102
votes
44
replies
7.7k
views
22 follow
What Are Numbers Every Bioinformatician Should Know?
knowledge career
updated 4 weeks ago by 38k • written 9.6 years ago by 24k
101
votes
81
replies
24k
views
17 follow
Duplicates on Illumina
duplicates illumina
updated 7 months ago by 127k • written 6.2 years ago by ★ 1.8k
100
votes
6
replies
22k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 17 days ago by 38k • written 4.6 years ago by 16k
100
votes
15
replies
97k
views
15 follow
Convertion Of Gff3 To Gtf
gtf gff
updated 27 days ago by ▴ 20 • written 10.8 years ago by 12k
100
votes
36
replies
27k
views
33 follow
Forum: List of cloud genomics companies
cloud-genomics
updated 9 days ago by ▴ 30 • written 9.4 years ago by ★ 3.6k
99
votes
16
replies
30k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 17 days ago by 38k • written 6.7 years ago by 26k
99
votes
31
replies
82k
views
18 follow
Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
bam picard samtools merge
updated 8 months ago by 38k • written 11.7 years ago by ★ 5.0k
99
votes
21
replies
7.9k
views
14 follow
Forum: How Has Bioinformatics Improved Over Time?
bioinformatics
updated 5 weeks ago by 38k • written 10.2 years ago by ▴ 370
97
votes
9
replies
113k
views
11 follow
How To Merge Two Fastq.Gz Files?
merge fastq
updated 11 months ago by ▴ 40 • written 9.5 years ago by ▴ 750
97
votes
23
replies
32k
views
15 follow
Is Tophat The Only Mapper To Consider For Rna-Seq Data?
bwa tophat rna-seq
updated 10 months ago by 38k • written 10.2 years ago by ▴ 330
97
votes
19
replies
87k
views
12 follow
How To Get The Sequence Of A Genomic Region From Ucsc?
sequence ucsc fasta
updated 7 months ago by 38k • written 13.1 years ago by 27k
94
votes
25
replies
31k
views
11 follow
Tutorial: Fastq Quality Control Shootout
quality qc trimming fastq
updated 5 weeks ago by 38k • written 10.5 years ago by 97k
94
votes
25
replies
74k
views
20 follow
Extract Sub-Set Of Regions From Vcf File
vcf tabix genome filter
updated 18 days ago by 2.6k • written 10.8 years ago by ▴ 820
93
votes
19
replies
56k
views
18 follow
What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
tree tool phylogenetics viewer
updated 10 months ago by ▴ 20 • written 12.6 years ago by ★ 2.6k
93
votes
50
replies
14k
views
17 follow
Forum: Fda Sends A Warning Letter To 23Andme - Personal Genomics Service Marketing To Be Discontinued
personal-genomics 23andMe
updated 4 weeks ago by 38k • written 9.4 years ago by 97k
92
votes
105
replies
34k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 18 days ago by 38k • written 4.6 years ago by 85k
92
votes
46
replies
10.0k
views
28 follow
Best Language For Introductory Programming Course From Within An Introduction Course On Bioinformatics.
programming subjective
updated 6 weeks ago by 38k • written 11.7 years ago by 3.2k
92
votes
20
replies
27k
views
13 follow
Is There Any R Or R / Bioconductor Package That Can Make Circular Plots Like Perl / Circos
r visualization
updated 10 months ago by 38k • written 11.1 years ago by ★ 1.5k
91
votes
25
replies
57k
views
18 follow
Best Practices/Softwares To Calculate Ka/Ks Ratio
kaks selection software
updated 6 months ago by 52k • written 12.1 years ago by 3.4k
91
votes
20
replies
18k
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 5 months ago by 38k • written 8.9 years ago by 20k
90
votes
44
replies
57k
views
28 follow
Tool to generate proportional Venn Diagrams?
visualization
updated 11 months ago by 38k • written 12.0 years ago by ★ 3.4k
90
votes
38
replies
129k
views
18 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 6 months ago by ▴ 10 • written 10.7 years ago by ▴ 370
89
votes
19
replies
30k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray bioconductor expression classification
updated 4 weeks ago by 38k • written 9.4 years ago by 20k
89
votes
31
replies
12k
views
23 follow
Best Graphics Gallery Or Blogs For Bioinformatics Use
graphs visualization genomics
updated 8 months ago by 38k • written 11.1 years ago by ★ 1.5k
1,000 results • Page 2 of 20
Recent Votes
Talk from Aaron Lun on Orchestrating Single-Cell Analysis With Bioconductor
SSPACE for scaffolding
Answer: Snakemake workflow for trimmomatic
Answer: How to remove duplicate reads after ONT basecalling from fastq.gz files
A: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p
A: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p
Answer: Getting Intron Positions from Amino Acid Sequences
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Recent Replies
Comment: How to deal with the probe id mapping to multiple gene ids? by GenoMax 127k
Where are you seeing this? [Platform file for this array][1] on GEO has these names uniquely assigned. [1]: https://www.ncbi.nlm.nih.go…
Comment: My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL by rpolicastro 11k
`Org.Mm.eg.db` is the mouse organism database, but your ENSEMBL IDs are for human genes. Mouse ensembl ids start with `ENSMUSG`. You proba…
Comment: Snakemake doesn't recognize output files even though they are created by DdogBoss • 0
Yes, it completed the dry run. What other information do you need?
Comment: LDSC correlation calculate confidence intervals by YL ▴ 10
Based on my personal thought, I think the se from LDSC output probably needs to be transferred using Delta method based on Fisher transform…
Comment: LDSC correlation calculate confidence intervals by YL ▴ 10
Hi, Are you able to find an answer for this? I have the exact question! YL
Answer: Gene duplicate by ATpoint 71k
Use use ensembID_geneName as gene identifier to avoid that. These duplicate names exist as genes so removing them is somewhat not really da…
Comment: Gene duplicate by Ram 38k
> some Ensembl IDs that are the same Please show us some examples.
Comment: R package for functional enrichment and depletion analysis by rpolicastro 11k
What you're describing is a simulation of the hypergeometric test, so if you want an exact solution you could use the function `fora` from …
Comment: How to remove duplicate reads after ONT basecalling from fastq.gz files by Darrenjdd • 0
Perfect! Thank you!
Comment: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p by Daniel • 0
Hi, I am wondering if you ever got an answer for this question. Also, I am curious why it is true that "All the reads coming from one end…
Answer: how can i filter a sam file from a paf file by Trivas ▴ 750
A quick search shows that `paf2sam` doesn't exist because a `.paf` file doesn't contain the CIGAR strings that `.sam` files have. A work ar…
Comment: What is the major problem with this pipeline of SNPs analysis? by Ram 38k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: What is the major problem with this pipeline of SNPs analysis? by Pierre Lindenbaum 153k
you can stick to gatk. But, again, using a GVCF without GenotypeGVCF is meaningless
Comment: Getting Intron Positions from Amino Acid Sequences by fafad046 • 0
thank you so so much, it worked! you are an absolute life savior :D
Answer: Getting Intron Positions from Amino Acid Sequences by GenoMax 127k
Using [**EntrezDirect**][1] (truncated because of space): $ esearch -db protein -query NP_001243728.1 | elink -target gene | efetch …
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