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1,000 results • Page 3 of 20
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115
votes
25
replies
32k
views
20 follow
Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
DESeq Kallisto RNASeq Salmon DESeq2
updated 11 days ago by 37k • written 7.7 years ago by ▴ 600
115
votes
18
replies
37k
views
14 follow
What Are The Best Bioinformatics Course Materials And Videos (Available Online)?
education online
updated 5.8 years ago by ▴ 20 • written 11.5 years ago by ★ 1.3k
113
votes
53
replies
4.7k
views
16 follow
Forum: Middle author, but not first author projects. How would you approach this?
career development authorship Forum
updated 3.8 years ago by ▴ 270 • written 3.8 years ago by ▴ 170
113
votes
7
replies
26k
views
7 follow
What Makes One Probability Distribution Better For Rna-Seq Than Another?
rna
updated 11.9 years ago by ▴ 140 • written 11.9 years ago by 21k
113
votes
34
replies
35k
views
18 follow
Forum: Snakemake vs. Nextflow: strengths and weaknesses
snakemake nextflow Forum
updated 3.5 years ago by ★ 9.2k • written 5.6 years ago by ▴ 760
112
votes
24
replies
44k
views
17 follow
Workflow Or Tutorial For Snp Calling?
snp samtools alignment next-gen sequencing
updated 5 months ago by 37k • written 11.7 years ago by ▴ 480
111
votes
24
replies
63k
views
12 follow
Is My Bam File Sorted ?
bam next-gen sequencing sort
updated 5.8 years ago by ▴ 170 • written 12.0 years ago by 152k
110
votes
37
replies
6.8k
views
13 follow
Bioinformatics Career Survey 2011/2012
career job
updated 11.0 years ago by 2.3k • written 11.3 years ago by 152k
108
votes
56
replies
39k
views
23 follow
Gene Fusion Detection: Rna-Seq Data
rna-seq next-gen sequencing fusion
updated 4 months ago by 37k • written 10.7 years ago by ▴ 380
107
votes
27
replies
26k
views
12 follow
Why You Need Perl/Python If You Know R/Shell [Ngs Data Analysis]
python next-gen
updated 12 months ago by 37k • written 10.8 years ago by 11k
106
votes
45
replies
79k
views
30 follow
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta
updated 5 months ago by ▴ 20 • written 10.5 years ago by ▴ 320
106
votes
23
replies
20k
views
16 follow
Forum: How Did You Learn Good Practice In Bioinformatics/Computational Biology?
bioinformatics Forum
written 9.0 years ago by ▴ 570
105
votes
27
replies
13k
views
14 follow
Is There Such A Thing As A Ucsc Api?
ucsc python comparative api
updated 20 months ago by ★ 1.5k • written 12.2 years ago by 2.3k
105
votes
26
replies
38k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation domain r
updated 4 months ago by 37k • written 10.0 years ago by ▴ 810
105
votes
72
replies
14k
views
17 follow
Digesting Fasta Sequences Into A Set Of Smaller Sequences
code fasta sequence codegolf
updated 4.3 years ago by 11k • written 12.5 years ago by 11k
105
votes
46
replies
11k
views
13 follow
Forum: Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
Forum
written 9.4 years ago by ★ 1.1k
105
votes
21
replies
19k
views
19 follow
Why Should I Use Galaxy ?
galaxy workflow
5.8 years ago by Pierre Lindenbaum 152k
103
votes
20
replies
28k
views
16 follow
What Wetlab Techniques Does A Bioinformatician Need To Be Able To Perform, If Any?
education meta
updated 11.9 years ago by ★ 1.6k • written 11.9 years ago by 3.2k
103
votes
12
replies
70k
views
7 follow
Bedtools Compare Multiple Bed Files?
bedtools intersect
updated 3 months ago by 37k • written 11.3 years ago by ★ 1.7k
102
votes
44
replies
7.7k
views
22 follow
What Are Numbers Every Bioinformatician Should Know?
bioinformatics
updated 2.1 years ago by 68k • written 9.5 years ago by 24k
102
votes
19
replies
17k
views
15 follow
How Does A Bioinformatics Scientist Document His/Her Work?
workflow bioinformatics
updated 10.7 years ago by ★ 2.1k • written 10.7 years ago by ▴ 830
102
votes
30
replies
59k
views
25 follow
Tools To Find Gene Ontology Term Enrichment
gene enrichment tool
updated 7 months ago by 37k • written 12.9 years ago by ★ 1.0k
100
votes
12
replies
36k
views
14 follow
Best Software For Detection Of Somatic Mutations From Matched Tumor:Normal Ngs Data
somatic-mutation variant-calling SNV
updated 16 months ago by 37k • written 10.9 years ago by ★ 2.8k
100
votes
81
replies
23k
views
17 follow
Duplicates on Illumina
duplicates illumina
updated 5 months ago by 125k • written 6.1 years ago by ★ 1.8k
99
votes
8
replies
26k
views
8 follow
Tutorial: Guide to TCGA data
TCGA cancer tools RNA-Seq clinical Tutorial
updated 6.2 years ago by ▴ 250 • written 6.9 years ago by ★ 1.1k
99
votes
24
replies
15k
views
16 follow
Workflow management software for pipeline development in NGS
pipeline workflow
updated 12 months ago by 37k • written 8.3 years ago by ▴ 310
99
votes
21
replies
7.8k
views
14 follow
Forum: How Has Bioinformatics Improved Over Time?
Forum
updated 8.7 years ago by 3.5k • written 10.0 years ago by ▴ 370
99
votes
44
replies
21k
views
33 follow
Best Free Text Editor For All Popular Languages (R, Python, Perl Etc..)
text r perl python
updated 5.4 years ago by ★ 2.5k • written 10.9 years ago by ★ 1.5k
99
votes
16
replies
75k
views
15 follow
How Much Coverage Do We Need For An Rna-Seq Experiment?
rna-seq coverage
8.2 years ago by Obi Griffith 20k
99
votes
36
replies
26k
views
32 follow
Forum: List of cloud genomics companies
cloud-genomics
updated 7 days ago by 21k • written 9.2 years ago by ★ 3.6k
98
votes
16
replies
29k
views
18 follow
Tutorial: Heatmaps in R
Tutorial R heatmap
9 months ago by Jean-Karim Heriche 26k
98
votes
6
replies
54k
views
6 follow
Insert Size And Fragment Size ?
15 months ago by Nicolas Rosewick 10k
98
votes
41
replies
4.3k
views
17 follow
Forum: I am really pissed off by the bioinformatics software world. Do/can we have a better solution?
software error sequencing next-gen Forum
updated 6.4 years ago by 96k • written 6.4 years ago by ▴ 500
98
votes
14
replies
95k
views
14 follow
Convertion Of Gff3 To Gtf
gtf gff
updated 10 months ago by 7.5k • written 10.7 years ago by 12k
97
votes
9
replies
110k
views
11 follow
How To Merge Two Fastq.Gz Files?
merge fastq
updated 9 months ago by ▴ 40 • written 9.4 years ago by ▴ 750
97
votes
35
replies
24k
views
16 follow
Disease Associated Snps
snp gwas database
updated 9.0 years ago by • 0 • written 12.7 years ago by ★ 1.4k
97
votes
23
replies
32k
views
15 follow
Is Tophat The Only Mapper To Consider For Rna-Seq Data?
bwa tophat rna-seq
updated 8 months ago by 37k • written 10.1 years ago by ▴ 330
97
votes
12
replies
47k
views
6 follow
Ensembl-Ids Vs. Entrez-Ids
ensembl entrez gene
updated 22 months ago by ▴ 10 • written 11.0 years ago by ▴ 420
97
votes
31
replies
79k
views
18 follow
Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
bam picard samtools merge
updated 6 months ago by 37k • written 11.6 years ago by ★ 5.0k
97
votes
19
replies
86k
views
12 follow
How To Get The Sequence Of A Genomic Region From Ucsc?
sequence ucsc fasta
updated 5 months ago by 37k • written 12.9 years ago by 27k
97
votes
26
replies
9.4k
views
15 follow
Do You Trust Bio-Xxx Projects ?
biopython bioperl biojava subjective
updated 12.0 years ago by 11k • written 12.0 years ago by ★ 2.2k
96
votes
26
replies
29k
views
15 follow
What Methods Do You Use For In/Del/Snp Calling?
sequencing short aligner snp
updated 9.2 years ago by 20 • written 12.8 years ago by 152k
95
votes
6
replies
21k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
snakemake conda workflow Tutorial
updated 2.2 years ago by ▴ 50 • written 4.4 years ago by 15k
94
votes
25
replies
31k
views
11 follow
Tutorial: Fastq Quality Control Shootout
quality fastq trimming qc tutorial Tutorial
updated 7 hours ago by 37k • written 10.4 years ago by 96k
94
votes
31
replies
36k
views
17 follow
What Is The Quickest Algorithm For Range Overlap?
python alignment next-gen sequencing database
updated 10 months ago by 37k • written 12.4 years ago by ▴ 280
93
votes
19
replies
55k
views
18 follow
What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
tree tool phylogenetics viewer
updated 8 months ago by ▴ 20 • written 12.4 years ago by ★ 2.6k
93
votes
31
replies
94k
views
20 follow
How To Split A Bam File By Chromosome
bam split chromosome
updated 11 months ago by ▴ 60 • written 10.7 years ago by ▴ 380
93
votes
21
replies
21k
views
13 follow
What Are The Advantages/Disadvantages Of One-Based Vs. Zero-Based Genome Coordinate Systems
coordinates genome
updated 8.2 years ago by 20 • written 11.9 years ago by 18k
93
votes
50
replies
14k
views
17 follow
Forum: Fda Sends A Warning Letter To 23Andme - Personal Genomics Service Marketing To Be Discontinued
Forum
updated 9.2 years ago by ▴ 370 • written 9.2 years ago by 96k
93
votes
32
replies
29k
views
26 follow
Linux Distros Best Suited For Bioinformatics?
linux
written 11.0 years ago by ▴ 150
1,000 results • Page 3 of 20
Recent Votes
Answer: Looking for a tool which provides mapping quality score distributions from BAM f
Comment: mirbase does not have miRNA annotation of my species, what are the alternatives?
Answer: mirbase does not have miRNA annotation of my species, what are the alternatives?
Answer: Gviz python alternative
Answer: Gviz python alternative
Answer: Annotating snps with gene information
Comment: Plotting Correlation matrix
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Recent Replies
Answer: Python Dictionary of Primer3-py Primer Designs by barslmn ★ 1.2k
You're so close. You can simply loop over sequence dictionaries like you did with the `design_output` and check if the keys with `startswit…
Comment: Unable to install clusterProfiler on Mac M1 by GenoMax 125k
Have you installed `Xcode` and the command line tools that go with? If not you will need to install those.
Answer: SRA taxonomy analysis by Steve • 0
Thanks @genomax I created an aws glue crawler to pull the data from s3://sra-pub-metadata-us-east-1/sra_tax_analysis_tool/ I wonder if it …
Comment: mirbase does not have miRNA annotation of my species, what are the alternatives? by demoraesdiogo2017 ▴ 80
thanks! however, shouldn't it also have a gtf/gff file with the annotations?
Comment: Getting a VCF file from plink .bed, .fam and .bim files by hi.there • 0
Thanks Ram. Yes. I have read all of this documentation before. --file and --bfile. I have actually tried doing the complete liftover be…
Answer: SRA taxonomy analysis by GenoMax 125k
This data may only be available using `BigQuery` for [**SRA in cloud**][1]. For more information on querying: https://www.ncbi.nlm.nih.g…
Comment: MesKit error message - Join columns must be present in data. by CH1374 • 0
column names for the maf are: [1] "Hugo_Symbol" "Chromosome" "Start_Position" [4] "End_Position" "Variant_Classification" "Variant_Type" [7…
Answer: scaffold assembly inro chromosomal assembly using reference genome by samuel.a.odonnell ▴ 450
Have a look at ragtag and ragout. I use ragout for smaller assemblies (~20 Mb and less) and ragtag for larger genomes.
Comment: CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRl by Ram 37k
I've been meaning to work on a Biostars-specific code formatting manual for a while now but the basic is pretty simple: You can use backtic…
Comment: Multiline Fasta To Single Line Fasta by Onur • 0
Thank you it's also worked for me too. Best,
Comment: CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRl by Estefania ▴ 10
Thanks Ram. Could you point to a manual on how to make the post look like yours? I just copy-pasted my R script and this is how it shows in…
Comment: extracting input files form Seurat by rasing02 • 0
Thank you jared.andrews07
Comment: extracting input files form Seurat by rasing02 • 0
Yes, I just need the input data so that investigators can use tools other than R to visualize the data in form of viloin plots or feature p…
Comment: Downloading 450k methylation data from GEO by GenoMax 125k
I don't think they have provided processed data as a single upload.
Answer: extracting input files form Seurat by jared.andrews07 ★ 14k
You can get the data behind any of the plots easily enough: ``` p <- VlnPlot(Seurat_object, features = "X", group.by = "Names",split.by…
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