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1,000 results • Page 2 of 20
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121
votes
54
replies
95k
views
23 follow
How to plot coverage and depth statistics of a bam file
bam coverage depth next-gen-sequencing
updated 5 weeks ago by ▴ 20 • written 9.3 years ago by ▴ 340
121
votes
35
replies
40k
views
20 follow
Forum: Snakemake vs. Nextflow: strengths and weaknesses
snakemake nextflow
updated 4 months ago by 40k • written 6.3 years ago by ▴ 790
120
votes
33
replies
37k
views
24 follow
Forum: Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 4 months ago by ★ 2.3k • written 10.1 years ago by 11k
118
votes
74
replies
43k
views
40 follow
Is there a Lims that doesn't suck?
LIMS
updated 10 months ago by 134k • written 12.8 years ago by ★ 3.3k
118
votes
26
replies
34k
views
22 follow
Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
DESeq Kallisto RNASeq Salmon DESeq2
updated 6 months ago by ▴ 80 • written 8.4 years ago by ▴ 610
117
votes
59
replies
31k
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 months ago by 40k • written 8.4 years ago by ▴ 30
116
votes
66
replies
43k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 6 months ago by 40k • written 5.2 years ago by 76k
116
votes
35
replies
7.6k
views
18 follow
Forum: Is Biostar Killing The Bioinformatics Core?
core biostars
updated 7 months ago by 40k • written 10.5 years ago by 21k
115
votes
25
replies
67k
views
14 follow
Is My Bam File Sorted ?
bam next-gen sequencing sort
updated 7 months ago by ▴ 10 • written 12.7 years ago by 157k
113
votes
53
replies
5.9k
views
16 follow
Forum: Middle author, but not first author projects. How would you approach this?
authorship career-development
updated 3 months ago by 40k • written 4.5 years ago by ▴ 170
110
votes
37
replies
7.4k
views
13 follow
Bioinformatics Career Survey 2011/2012
career
updated 7 months ago by 40k • written 12.0 years ago by 157k
106
votes
23
replies
21k
views
16 follow
Forum: How Did You Learn Good Practice In Bioinformatics/Computational Biology?
bioinformatics
updated 6 months ago by 40k • written 9.6 years ago by ▴ 590
105
votes
26
replies
40k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation domain r
updated 7 days ago by 11k • written 10.7 years ago by ▴ 810
105
votes
46
replies
12k
views
13 follow
Forum: Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
epigenetics
updated 6 months ago by 40k • written 10.1 years ago by ★ 1.1k
104
votes
6
replies
24k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 6 months ago by 40k • written 5.1 years ago by 16k
104
votes
12
replies
76k
views
7 follow
Bedtools Compare Multiple Bed Files?
bedtools intersect
updated 11 months ago by 40k • written 11.9 years ago by ★ 1.7k
102
votes
19
replies
17k
views
15 follow
How Does A Bioinformatics Scientist Document His/Her Work?
workflow
updated 7 months ago by 40k • written 11.3 years ago by ▴ 830
102
votes
44
replies
8.3k
views
22 follow
What Are Numbers Every Bioinformatician Should Know?
knowledge career
updated 7 months ago by 40k • written 10.1 years ago by 24k
102
votes
30
replies
60k
views
25 follow
Tools To Find Gene Ontology Term Enrichment
gene enrichment
updated 3 months ago by 40k • written 13.6 years ago by ★ 1.0k
100
votes
38
replies
29k
views
34 follow
Forum: List of cloud genomics companies
cloud-genomics
updated 26 days ago by 21k • written 9.9 years ago by ★ 3.6k
100
votes
15
replies
104k
views
15 follow
Convertion Of Gff3 To Gtf
gtf gff
updated 6 months ago by ▴ 20 • written 11.3 years ago by 12k
99
votes
8
replies
28k
views
8 follow
Tutorial: Guide to TCGA data
cancer RNA-Seq clinical TCGA
updated 5 months ago by 40k • written 7.6 years ago by ★ 1.1k
99
votes
32
replies
105k
views
21 follow
How To Split A Bam File By Chromosome
bam split chromosome
updated 6 weeks ago by • 0 • written 11.3 years ago by ▴ 390
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
99
votes
16
replies
31k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 6 months ago by 40k • written 7.1 years ago by 26k
98
votes
41
replies
5.0k
views
17 follow
Forum: I am really pissed off by the bioinformatics software world. Do/can we have a better solution?
software-error next-gen-sequencing
updated 5 months ago by 40k • written 7.1 years ago by ▴ 510
97
votes
27
replies
81k
views
21 follow
Extract Sub-Set Of Regions From Vcf File
vcf tabix genome filter
updated 4 months ago by • 0 • written 11.3 years ago by ▴ 820
95
votes
25
replies
32k
views
11 follow
Tutorial: Fastq Quality Control Shootout
quality qc trimming fastq
updated 7 months ago by 40k • written 11.0 years ago by 98k
93
votes
105
replies
39k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 6 months ago by 40k • written 5.1 years ago by 86k
93
votes
19
replies
57k
views
18 follow
What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
phylogenetics-tree
updated 3 months ago by 40k • written 13.0 years ago by ★ 2.6k
93
votes
39
replies
142k
views
19 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 5 months ago by ▴ 140 • written 11.2 years ago by ▴ 380
93
votes
50
replies
15k
views
17 follow
Forum: Fda Sends A Warning Letter To 23Andme - Personal Genomics Service Marketing To Be Discontinued
personal-genomics 23andMe
updated 6 months ago by 40k • written 9.8 years ago by 98k
92
votes
18
replies
63k
views
12 follow
Sequence length from Fasta
fasta
updated 9 months ago by 40k • written 8.9 years ago by ▴ 80
92
votes
46
replies
11k
views
28 follow
Best Language For Introductory Programming Course From Within An Introduction Course On Bioinformatics.
programming subjective
updated 7 months ago by 40k • written 12.2 years ago by 3.2k
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
90
votes
16
replies
21k
views
15 follow
Are we tricking ourselves with batch effect correction?
combat batch-effect sva
updated 7 months ago by ▴ 20 • written 8.3 years ago by ★ 3.0k
90
votes
19
replies
31k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray bioconductor expression classification
updated 6 months ago by 40k • written 9.9 years ago by 20k
89
votes
13
replies
20k
views
9 follow
What Do Different Bioinformatics Positions Mean?
career general
updated 7 months ago by 40k • written 13.5 years ago by ★ 1.6k
88
votes
24
replies
5.1k
views
10 follow
Forum: How To Be Helpful As A Biostar Moderator/Editor?
biostars
updated 7 months ago by 40k • written 10.6 years ago by 1.9k
86
votes
22
replies
80k
views
14 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 11 weeks ago by • 0 • written 5.2 years ago by ▴ 580
86
votes
29
replies
9.1k
views
9 follow
Forum: What is the future of EMBL-EBI (and European bioinformatics in general) in case of a 'Brexit'?
EU brexit EBI politics
updated 5 months ago by 40k • written 7.3 years ago by 53k
85
votes
16
replies
89k
views
9 follow
Number of mapped reads from BAM file
bam sam reads mapping
updated 10 months ago by ▴ 50 • written 8.5 years ago by ★ 2.7k
85
votes
2
replies
56k
views
6 follow
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 7 months ago by 40k • written 10.2 years ago by 11k
84
votes
21
replies
18k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 6 months ago by 40k • written 2.9 years ago by 3.0k
84
votes
29
replies
30k
views
20 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 9 weeks ago by • 0 • written 7.5 years ago by 20k
84
votes
22
replies
4.0k
views
12 follow
Forum: is fortran still used in bioinformatics?
FORTRAN R
updated 6 months ago by 40k • written 4.3 years ago by ▴ 180
83
votes
34
replies
17k
views
22 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment R pathway active-subnetwork
updated 4 months ago by • 0 • written 5.3 years ago by ★ 1.3k
83
votes
20
replies
18k
views
17 follow
How Do Pathway Databases Compare?
pathway database subjective
updated 9 weeks ago by ▴ 30 • written 12.9 years ago by ▴ 470
82
votes
32
replies
7.0k
views
13 follow
Forum: Shall We Go Back To Stackexchange?
meta
updated 7 months ago by 40k • written 10.8 years ago by ★ 3.6k
82
votes
19
replies
12k
views
8 follow
Future Directions In Bioinformatics
subjective career
updated 7 months ago by 40k • written 12.9 years ago by ★ 1.5k
1,000 results • Page 2 of 20
Recent Votes
Answer: Samtools Failing to Install through Conda
Answer: Importance of Data Structures for Bioinformatics?
Answer: Filter transcription factors
Comment: Low Alignment rate
Comment: Understanding TCGA barcodes with dot in the fieldname
Answer: Filter transcription factors
Answer: How to sort cd-hit-est cluster file
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Recent Replies
Answer: Samtools Failing to Install through Conda by hukai916 ▴ 10
Same issue on brand new M2 chip MacBook: conda seems NOT able to find `samtools`; `brew` worked.
Comment: Enrichment of mitochondrial and ribosomal pathways - an artifact? by LauferVA 3.7k
im unclear on why you would ask this question without providing more context about the cell states that are being explored by the experimen…
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool? by Ram 40k
Singularity is a good option but OP explicitly mentions that their users are using their own laptops. On laptops, it's a lot easier to use …
Comment: Calculation of TMB on gene level by Zhenyu Zhang ▴ 980
It's what you asked for just mutation frequency or mutation frequency adjusted by gene length?
Comment: Understanding TCGA barcodes with dot in the fieldname by Zhenyu Zhang ▴ 980
second this. The "95FC84F5-4FB3-4CE7-ACD0-C7E0D8F03DD7" is obviously an UUID, not related to TCGA barcode
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool? by Yogi ▴ 10
Just 1 thing to consider. `Docker` is great because it provides a way to containerize applications. HOWEVER, many people on computation…
Comment: Filter human transcription factors by Yogi ▴ 10
Definitely the best resource. Was also going to recommend this one.
Comment: GO analysis after DESeq2 by Ram 40k
The go category needs to be a [facet][1] on the ggplot. [1]: http://www.sthda.com/english/wiki/ggplot2-facet-split-a-plot-into-a-matrix-…
Comment: How to sort cd-hit-est cluster file by Mo ▴ 40
Hi, Thank you so much, this has worked :)
Comment: Program for Overlapping DMRs (Differentially Methylated Regions) Between Groups by LChart 3.3k
You might specify how the data is formatted. If you have `chr start end` columns, you can use `bedtools` to perform the interval operations.
Comment: RepeatMasker error when trying to generate repeat sequence distribution pie char by epianalysis • 0
Do you mind telling me how you were able to create a custom txdb object that sufficiently annotates repeats?
Comment: obtaining circular RNAs' sequences from circBase by aminijavad4 ▴ 10
I didn't know
Comment: obtaining circular RNAs' sequences from circBase by aminijavad4 ▴ 10
Thank you for your reply, Barry. Upon further searching, I discovered that circular RNA sequences can be downloaded from the downloads sect…
Answer: Saving the output of LD pruning from SNPRelate package as a new GDS file by James W. MacDonald ▴ 20
You want `createDataFile` from `GWASTools`. Ideally you wouldn't do that though - it takes forever to create a new GDS file, and the whole …
Comment: Calculation of TMB on gene level by ATpoint 76k
The poster is spamming chatgpt for some time. No value in that, but also not forbidden by any forum rule that I am aware of, so other than …
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