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117
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59
replies
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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 9 months ago by 41k • written 8.6 years ago by ▴ 30
116
votes
25
replies
68k
views
14 follow
Is My Bam File Sorted ?
bam next-gen sequencing sort
updated 9 months ago by ▴ 20 • written 12.8 years ago by 158k
116
votes
18
replies
39k
views
14 follow
What Are The Best Bioinformatics Course Materials And Videos (Available Online)?
education online
updated 6.6 years ago by ▴ 20 • written 12.3 years ago by ★ 1.3k
116
votes
35
replies
7.8k
views
18 follow
Forum: Is Biostar Killing The Bioinformatics Core?
core biostars
updated 9 months ago by 41k • written 10.7 years ago by 22k
115
votes
21
replies
112k
views
14 follow
When To Choose Python Over Perl (And Vice Versa)?
python perl comparison
updated 11.7 years ago by ▴ 30 • written 12.1 years ago by ★ 2.6k
114
votes
7
replies
27k
views
7 follow
What Makes One Probability Distribution Better For Rna-Seq Than Another?
rna
updated 12.8 years ago by ▴ 140 • written 12.8 years ago by 22k
113
votes
53
replies
6.3k
views
16 follow
Forum: Middle author, but not first author projects. How would you approach this?
authorship career-development
updated 6 months ago by 41k • written 4.7 years ago by ▴ 170
112
votes
24
replies
46k
views
17 follow
Workflow Or Tutorial For Snp Calling?
snp samtools alignment next-gen sequencing
updated 15 months ago by 41k • written 12.6 years ago by ▴ 480
110
votes
37
replies
7.7k
views
13 follow
Bioinformatics Career Survey 2011/2012
career
updated 9 months ago by 41k • written 12.2 years ago by 158k
110
votes
56
replies
42k
views
23 follow
Gene Fusion Detection: Rna-Seq Data
rna-seq next-gen sequencing fusion
updated 14 months ago by 41k • written 11.5 years ago by ▴ 380
108
votes
45
replies
84k
views
30 follow
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta
updated 15 months ago by ▴ 40 • written 11.4 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 23 months ago by 41k • written 11.6 years ago by 11k
106
votes
23
replies
21k
views
16 follow
Forum: How Did You Learn Good Practice In Bioinformatics/Computational Biology?
bioinformatics
updated 9 months ago by 41k • written 9.8 years ago by ▴ 590
105
votes
46
replies
12k
views
13 follow
Forum: Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
epigenetics
updated 9 months ago by 41k • written 10.3 years ago by ★ 1.1k
105
votes
21
replies
20k
views
19 follow
Why Should I Use Galaxy ?
galaxy workflow
6.6 years ago by Pierre Lindenbaum 158k
105
votes
72
replies
16k
views
17 follow
Digesting Fasta Sequences Into A Set Of Smaller Sequences
code fasta sequence codegolf
updated 5.2 years ago by 11k • written 13.4 years ago by 11k
105
votes
26
replies
41k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation domain r
updated 10 weeks ago by 11k • written 10.9 years ago by ▴ 810
105
votes
31
replies
90k
views
18 follow
Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
bam picard samtools merge
updated 16 months ago by 41k • written 12.4 years ago by ★ 5.1k
105
votes
27
replies
14k
views
14 follow
Is There Such A Thing As A Ucsc Api?
ucsc python comparative api
updated 2.5 years ago by ★ 1.6k • written 13.1 years ago by 2.3k
104
votes
12
replies
77k
views
7 follow
Bedtools Compare Multiple Bed Files?
bedtools intersect
updated 13 months ago by 41k • written 12.1 years ago by ★ 1.7k
104
votes
6
replies
24k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 8 months ago by 41k • written 5.2 years ago by 16k
103
votes
20
replies
29k
views
16 follow
What Wetlab Techniques Does A Bioinformatician Need To Be Able To Perform, If Any?
education meta
updated 12.7 years ago by ★ 1.6k • written 12.7 years ago by 3.2k
102
votes
44
replies
8.6k
views
22 follow
What Are Numbers Every Bioinformatician Should Know?
knowledge career
updated 9 months ago by 41k • written 10.3 years ago by 24k
102
votes
30
replies
61k
views
25 follow
Tools To Find Gene Ontology Term Enrichment
gene enrichment
updated 5 weeks ago by 41k • written 13.7 years ago by ★ 1.0k
102
votes
19
replies
18k
views
15 follow
How Does A Bioinformatics Scientist Document His/Her Work?
workflow
updated 9 months ago by 41k • written 11.5 years ago by ▴ 830
102
votes
81
replies
29k
views
17 follow
Duplicates on Illumina
duplicates illumina
updated 15 months ago by 136k • written 6.9 years ago by ★ 1.9k
101
votes
34
replies
108k
views
23 follow
How To Split A Bam File By Chromosome
bam split chromosome
updated 8 weeks ago by 14k • written 11.5 years ago by ▴ 390
100
votes
15
replies
107k
views
15 follow
Convertion Of Gff3 To Gtf
gtf gff
updated 9 months ago by ▴ 20 • written 11.5 years ago by 12k
100
votes
6
replies
60k
views
6 follow
Insert Size And Fragment Size ?
2.1 years ago by Nicolas Rosewick 10k
100
votes
38
replies
29k
views
34 follow
Forum: List of cloud genomics companies
cloud-genomics
updated 9 days ago by 22k • written 10.1 years ago by ★ 3.6k
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 2.2 years ago by 41k • written 11.7 years ago by ★ 2.8k
99
votes
8
replies
28k
views
8 follow
Tutorial: Guide to TCGA data
cancer RNA-Seq clinical TCGA
updated 8 months ago by 41k • written 7.8 years ago by ★ 1.1k
99
votes
16
replies
76k
views
15 follow
How Much Coverage Do We Need For An Rna-Seq Experiment?
rna-seq coverage
9.0 years ago by Obi Griffith 20k
99
votes
24
replies
16k
views
16 follow
Workflow management software for pipeline development in NGS
pipeline workflow
updated 22 months ago by 41k • written 9.1 years ago by ▴ 310
99
votes
16
replies
32k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 8 months ago by 41k • written 7.3 years ago by 26k
99
votes
21
replies
8.6k
views
14 follow
Forum: How Has Bioinformatics Improved Over Time?
bioinformatics
updated 9 months ago by 41k • written 10.8 years ago by ▴ 370
99
votes
9
replies
122k
views
11 follow
How To Merge Two Fastq.Gz Files?
merge fastq
updated 19 months ago by ▴ 40 • written 10.2 years ago by ▴ 750
99
votes
44
replies
23k
views
33 follow
Best Free Text Editor For All Popular Languages (R, Python, Perl Etc..)
text r perl python
updated 6.2 years ago by ★ 2.6k • written 11.7 years ago by ★ 1.5k
98
votes
27
replies
84k
views
21 follow
Extract Sub-Set Of Regions From Vcf File
vcf tabix genome filter
updated 6 months ago by • 0 • written 11.5 years ago by ▴ 830
98
votes
12
replies
51k
views
6 follow
Ensembl-Ids Vs. Entrez-Ids
ensembl entrez gene
updated 2.7 years ago by ▴ 10 • written 11.9 years ago by ▴ 420
98
votes
41
replies
5.4k
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 7 months ago by 41k • written 7.3 years ago by ▴ 510
97
votes
26
replies
10k
views
15 follow
Do You Trust Bio-Xxx Projects ?
biopython bioperl biojava subjective
updated 12.9 years ago by 11k • written 12.9 years ago by ★ 2.2k
97
votes
19
replies
92k
views
12 follow
How To Get The Sequence Of A Genomic Region From Ucsc?
ucsc fasta sequence
updated 6 weeks ago by 41k • written 13.8 years ago by 28k
97
votes
23
replies
33k
views
15 follow
Is Tophat The Only Mapper To Consider For Rna-Seq Data?
bwa tophat rna-seq
updated 18 months ago by 41k • written 10.9 years ago by ▴ 330
97
votes
35
replies
25k
views
16 follow
Disease Associated Snps
snp gwas database
updated 9.9 years ago by • 0 • written 13.5 years ago by ★ 1.5k
96
votes
26
replies
31k
views
15 follow
What Methods Do You Use For In/Del/Snp Calling?
short-read-aligner snp sequencing
updated 21 days ago by 41k • written 13.7 years ago by 158k
95
votes
105
replies
41k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 8 months ago by 41k • written 5.3 years ago by 86k
95
votes
25
replies
32k
views
11 follow
Tutorial: Fastq Quality Control Shootout
quality qc trimming fastq
updated 9 months ago by 41k • written 11.2 years ago by 99k
95
votes
5
replies
53k
views
Difference between Hard Clip and Soft Clip in Samtools CIGAR string
samtools clipped-reads soft-clip bam hard-clip
updated 23 months ago by 41k • written 9.3 years ago by ★ 2.5k
95
votes
6
replies
36k
views
In Sam Format, Clarify The Meaning Of The "0" Flag.
sam
updated 12.7 years ago by ★ 1.4k • written 12.7 years ago by ▴ 580
113,889 results • Page 3 of 2278
Recent Votes
Comment: Problematic fastq files...How can we trust them?
Answer: GO categorization
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: An incomprehensible error with R package gggenes
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Popular Question to endre.sebestyen ▴ 10
Popular Question to beausoleilmo ▴ 560
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Recent Replies
Comment: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates with by GenoMax 136k
Yes that should be true. I will let https://www.biostars.org/u/14684/ confirm.
Comment: From TPM to raw counts by Gama313 ▴ 120
Thanks for the answe and the linkI used bioinfokit tpm formula to calculate tpm from bulk which is the same formula given in your link: A= …
Comment: From TPM to raw counts by Gama313 ▴ 120
Thanks Brian for the suggestion. However, I did the whole process, from bulk counts generation, to data transformation and scrna deconvolut…
Answer: Are 10x cellranger-arc ATAC bam files deduplicated? by swbarnes2 13k
My experience with regular 10x bam files is that duplicates are not removed, but they are flagged as duplicates. So take a look at the …
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo by fluke • 0
Thanks a lot for your answer, I’m confused between RSEM expected count and RSEM normalized count. I’m working on this dataset from UCSC ht…
Answer: From TPM to raw counts by Istvan Albert 99k
In principle, the TPM formula can be reverted, see the timeless post * [What the FPKM? A review of RNA-Seq expression units][1] In p…
Comment: Low coverage whole genome sequencing reveal excess heterozygosity for multiple S by beausoleilmo ▴ 560
You're right, I wasn't explaining the problem clearly. Thanks for the directions! - The depth; coverage ~3.00X ± 2.50 SD - The sequen…
Comment: Using metagenome assembly and binning to identify and mitigate contamination in by Mensur Dlakic ★ 25k
All good points, especially about multiple copies of single-copy genes. I am doing error-correction in my assemblies, but was making an edu…
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo by CTLong ▴ 20
Yes, normalized RSEM counts from TCGA can be used as input for Limma Voom. Please check this post https://support.bioconductor.org/p/63981/…
Comment: How to obtain data on the coordinates of the Exon region from UCSC by ayasu • 0
Sorry for the delay in expressing my thanks. I found the advice to look at the information from MySQL very useful. I will also refer to t…
Comment: From TPM to raw counts by Brian Bushnell 19k
I'm posting this as a comment instead of an answer specifically because it's just what I would do and I don't know if it's the best approac…
Comment: Using metagenome assembly and binning to identify and mitigate contamination in by Brian Bushnell 19k
In most cases error-correction should take care of error-spawned fake minor alleles, though... > If you want to convince yourself of this,…
Answer: Using metagenome assembly and binning to identify and mitigate contamination in by Mensur Dlakic ★ 25k
It is a valid question, and I particularly like when posters err on the side of providing more than less detail. Metagenomic binning can be…
Answer: Low coverage whole genome sequencing reveal excess heterozygosity for multiple S by Brian Bushnell 19k
I don't understand your plot. Perhaps a legend would help? I also don't know what you mean by "genotype frequency"; is that the ratio of …
Comment: Does GNOMAD use all LOFTEE LoF filters? by AMARU • 0
Can you post the commands you used? I am having some issues running that plugin on vep v110. It appears in fields but it doesn't annotat…
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