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117
votes
66
replies
46k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 13 months ago by 43k • written 5.8 years ago by 81k
117
votes
18
replies
40k
views
14 follow
What Are The Best Bioinformatics Course Materials And Videos (Available Online)?
education online
updated 7.0 years ago by ▴ 20 • written 12.7 years ago by ★ 1.3k
116
votes
35
replies
8.2k
views
18 follow
Forum: Is Biostar Killing The Bioinformatics Core?
core biostars
updated 14 months ago by 43k • written 11.0 years ago by 22k
116
votes
25
replies
69k
views
14 follow
Is My Bam File Sorted ?
bam next-gen sequencing sort
updated 14 months ago by ▴ 20 • written 13.2 years ago by 161k
115
votes
21
replies
113k
views
14 follow
When To Choose Python Over Perl (And Vice Versa)?
python perl comparison
updated 12.1 years ago by ▴ 30 • written 12.5 years ago by ★ 2.6k
114
votes
7
replies
28k
views
7 follow
What Makes One Probability Distribution Better For Rna-Seq Than Another?
rna
updated 13.1 years ago by ▴ 140 • written 13.1 years ago by 22k
113
votes
53
replies
7.0k
views
16 follow
Forum: Middle author, but not first author projects. How would you approach this?
authorship career-development
updated 10 months ago by 43k • written 5.0 years ago by ▴ 170
112
votes
24
replies
47k
views
17 follow
Workflow Or Tutorial For Snp Calling?
snp samtools alignment next-gen sequencing
updated 19 months ago by 43k • written 12.9 years ago by ▴ 480
112
votes
56
replies
44k
views
23 follow
Gene Fusion Detection: Rna-Seq Data
rna-seq next-gen sequencing fusion
updated 19 months ago by 43k • written 11.9 years ago by ▴ 380
110
votes
37
replies
8.4k
views
13 follow
Bioinformatics Career Survey 2011/2012
career
updated 14 months ago by 43k • written 12.6 years ago by 161k
108
votes
45
replies
86k
views
30 follow
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta
updated 19 months ago by ▴ 70 • written 11.7 years ago by ▴ 320
107
votes
27
replies
27k
views
12 follow
Why You Need Perl/Python If You Know R/Shell [Ngs Data Analysis]
python next-gen
updated 2.3 years ago by 43k • written 12.0 years ago by 11k
106
votes
6
replies
26k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 13 months ago by 43k • written 5.6 years ago by 16k
106
votes
27
replies
15k
views
14 follow
Is There Such A Thing As A Ucsc Api?
ucsc python comparative api
updated 2.9 years ago by ★ 1.6k • written 13.4 years ago by 2.3k
106
votes
23
replies
22k
views
16 follow
Forum: How Did You Learn Good Practice In Bioinformatics/Computational Biology?
bioinformatics
updated 13 months ago by 43k • written 10.2 years ago by ▴ 590
106
votes
12
replies
80k
views
7 follow
Bedtools Compare Multiple Bed Files?
bedtools intersect
updated 18 months ago by 43k • written 12.5 years ago by ★ 1.7k
105
votes
26
replies
43k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation domain r
updated 7 months ago by 11k • written 11.3 years ago by ▴ 810
105
votes
31
replies
94k
views
18 follow
Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
bam picard samtools merge
updated 4 months ago by ▴ 450 • written 12.8 years ago by ★ 5.1k
105
votes
72
replies
18k
views
17 follow
Digesting Fasta Sequences Into A Set Of Smaller Sequences
code fasta sequence codegolf
updated 5.5 years ago by 11k • written 13.7 years ago by 11k
105
votes
46
replies
13k
views
13 follow
Forum: Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
epigenetics
updated 13 months ago by 43k • written 10.6 years ago by ★ 1.1k
105
votes
21
replies
21k
views
19 follow
Why Should I Use Galaxy ?
galaxy workflow
7.0 years ago by Pierre Lindenbaum 161k
105
votes
81
replies
32k
views
17 follow
Duplicates on Illumina
duplicates illumina
updated 19 months ago by 141k • written 7.3 years ago by ★ 1.9k
105
votes
15
replies
112k
views
16 follow
Convertion Of Gff3 To Gtf
gtf gff
updated 4 weeks ago by ▴ 140 • written 11.9 years ago by 12k
103
votes
20
replies
30k
views
16 follow
What Wetlab Techniques Does A Bioinformatician Need To Be Able To Perform, If Any?
education meta
updated 13.1 years ago by ★ 1.6k • written 13.1 years ago by 3.2k
103
votes
34
replies
113k
views
23 follow
How To Split A Bam File By Chromosome
bam
updated 3 months ago by 43k • written 11.9 years ago by ▴ 390
103
votes
27
replies
88k
views
21 follow
Extract Sub-Set Of Regions From Vcf File
vcf tabix genome filter
updated 11 months ago by • 0 • written 11.9 years ago by ▴ 830
103
votes
42
replies
31k
views
34 follow
Forum: List of cloud genomics companies
cloud-genomics
updated 11 days ago by 22k • written 10.4 years ago by ★ 3.6k
102
votes
30
replies
62k
views
25 follow
Tools To Find Gene Ontology Term Enrichment
gene enrichment
updated 5 months ago by 43k • written 14.1 years ago by ★ 1.0k
102
votes
44
replies
9.0k
views
22 follow
What Are Numbers Every Bioinformatician Should Know?
knowledge career
updated 13 months ago by 43k • written 10.7 years ago by 24k
102
votes
19
replies
18k
views
15 follow
How Does A Bioinformatics Scientist Document His/Her Work?
workflow
updated 14 months ago by 43k • written 11.9 years ago by ▴ 830
100
votes
6
replies
63k
views
6 follow
Insert Size And Fragment Size ?
2.5 years ago by Nicolas Rosewick 10k
100
votes
16
replies
77k
views
15 follow
How Much Coverage Do We Need For An Rna-Seq Experiment?
rna-seq coverage
9.4 years ago by Obi Griffith 20k
100
votes
12
replies
37k
views
14 follow
Best Software For Detection Of Somatic Mutations From Matched Tumor:Normal Ngs Data
somatic-mutation variant-calling SNV
updated 2.6 years ago by 43k • written 12.1 years ago by ★ 2.8k
100
votes
9
replies
127k
views
11 follow
How To Merge Two Fastq.Gz Files?
merge fastq
updated 24 months ago by ▴ 40 • written 10.6 years ago by ▴ 760
99
votes
8
replies
29k
views
8 follow
Tutorial: Guide to TCGA data
cancer RNA-Seq clinical TCGA
updated 12 months ago by 43k • written 8.1 years ago by ★ 1.1k
99
votes
21
replies
8.9k
views
14 follow
Forum: How Has Bioinformatics Improved Over Time?
bioinformatics
updated 14 months ago by 43k • written 11.2 years ago by ▴ 370
99
votes
16
replies
33k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 13 months ago by 43k • written 7.7 years ago by 27k
99
votes
44
replies
24k
views
33 follow
Best Free Text Editor For All Popular Languages (R, Python, Perl Etc..)
text r perl python
updated 6.6 years ago by ★ 2.6k • written 12.1 years ago by ★ 1.5k
99
votes
24
replies
17k
views
16 follow
Workflow management software for pipeline development in NGS
pipeline workflow
updated 2.2 years ago by 43k • written 9.5 years ago by ▴ 310
98
votes
106
replies
46k
views
26 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 11 days ago by ▴ 20 • written 5.6 years ago by 87k
98
votes
41
replies
6.1k
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 12 months ago by 43k • written 7.6 years ago by ▴ 510
98
votes
39
replies
156k
views
19 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 12 months ago by ▴ 180 • written 11.8 years ago by ▴ 390
98
votes
12
replies
53k
views
6 follow
Ensembl-Ids Vs. Entrez-Ids
ensembl entrez gene
updated 3.1 years ago by ▴ 10 • written 12.3 years ago by ▴ 420
97
votes
23
replies
33k
views
15 follow
Is Tophat The Only Mapper To Consider For Rna-Seq Data?
bwa tophat rna-seq
updated 23 months ago by 43k • written 11.3 years ago by ▴ 330
97
votes
26
replies
11k
views
15 follow
Do You Trust Bio-Xxx Projects ?
biopython bioperl biojava subjective
updated 13.2 years ago by 11k • written 13.2 years ago by ★ 2.2k
97
votes
35
replies
26k
views
16 follow
Disease Associated Snps
snp gwas database
updated 10.2 years ago by • 0 • written 13.9 years ago by ★ 1.5k
97
votes
19
replies
94k
views
12 follow
How To Get The Sequence Of A Genomic Region From Ucsc?
ucsc fasta sequence
updated 6 months ago by 43k • written 14.2 years ago by 28k
96
votes
26
replies
31k
views
15 follow
What Methods Do You Use For In/Del/Snp Calling?
short-read-aligner snp sequencing
updated 5 months ago by 43k • written 14.0 years ago by 161k
95
votes
25
replies
33k
views
11 follow
Tutorial: Fastq Quality Control Shootout
quality qc trimming fastq
updated 14 months ago by 43k • written 11.6 years ago by 100k
95
votes
6
replies
37k
views
In Sam Format, Clarify The Meaning Of The "0" Flag.
sam
updated 13.0 years ago by ★ 1.4k • written 13.0 years ago by ▴ 580
1,000 results • Page 3 of 20
Recent Votes
bcftools multiple commands
bcftools pipe generated file from first command with second
C: How to setup a Summarized Experiment
A: How to download genome assemblies from NCBI with a list of GCA identifiers?
what's the genomic location and name of gene responsible for orange and black patches in calico cats
Comment: featureCounts --primary tag counting uniquely mapped reads and excludes multi-ma
Answer: Duplicate marking, read names, and the SRA
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Recent Replies
Comment: how to find genes that are significantly expressed in brain cortex samples by Ram 43k
Can you explain the normalization or give me a link that describes it, please? Comparison across samples will always be caveated as RNA-seq…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach by Ram 43k
Sorry, I see how harsh I come across. It's not good practice to use multiple versions of R in the same project. I can understand legacy pro…
Answer: MEGA Analysis Issue on High-Performance Computer by Mensur Dlakic ★ 27k
> I have ensured that I am using the latest version of MEGA and that other applications are not consuming excessive resources during the an…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach by BioinfGuru ★ 1.7k
Some of us are still learning and fall foul to knowledge limitation fairly regularly. Luckily we have people to put us in our place.
Answer: Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits by GenoMax 141k
> I know that I should be able to collect protein sequences from the blastp results into a file, but I do not know how to do this. You c…
Comment: how to find genes that are significantly expressed in brain cortex samples by rheab1230 ▴ 140
I got the normalized gene count from gtex portal. they use inverse quantile normalization
Comment: what's the genomic location and name of gene responsible for orange and black pa by Matthias Zepper 4.5k
It is not entirely off, but evidently also not correct. Melanin biosynthesis is a multistep process, that indeed prominently involves the…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach by Ram 43k
> so a single Rscript could utilise multiple environments and versions How is that sane, let alone "better"? Also, why use `snap` for curl…
Comment: how to find genes that are significantly expressed in brain cortex samples by Ram 43k
Normalized how?
Comment: Duplicate marking, read names, and the SRA by GenoMax 141k
With public data one has to work with what is there. If the information about position is absent then only thing that could be done is to l…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach by BioinfGuru ★ 1.7k
Or better yet. To have an R package that allows access to conda environments via "conda list env" so that environments can be switched with…
Comment: what's the genomic location and name of gene responsible for orange and black pa by GenoMax 141k
If GPT is right then it says that: > The specific gene responsible for the orange and non-orange (black or > gray) fur colors in cats is t…
Comment: what's the genomic location and name of gene responsible for orange and black pa by Jean-Karim Heriche 27k
As far as I know the Orange locus hasn't been mapped to a gene. Maybe this paper will help in narrowing the search: https://www.ncbi.nlm.ni…
Comment: Duplicate marking, read names, and the SRA by Luka • 0
>Curios if there a reference for this? [Apparently it's not deprecated yet][1], but will be soon and the SRA intends for it to be at some …
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach by Ram 43k
I prefer RStudio for new projects as well. The moment I need versions though, RStudio becomes a burden. I wish one could launch RStudio fro…
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