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31
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34
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5.7k
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11 follow
Forum: pros- and cons- : programming skills vs. GUI
Forum programming lecture
updated 23 months ago by 38k • written 7.3 years ago by ★ 4.6k
30
votes
34
replies
5.2k
views
enrichment of gene set with enrichR
enrichR RNA-Seq R
updated 5.0 years ago by 47k • written 5.0 years ago by ▴ 30
16
votes
34
replies
3.6k
views
7 follow
GC percent detection for several number of genes
GC% large number of genes
6.0 years ago by nazaninhoseinkhan ▴ 490
16
votes
34
replies
11k
views
6 follow
Why am I unable to load my data from a tab separated file into R?
microarray programming R
updated 11 months ago by 38k • written 8.1 years ago by ▴ 920
79
votes
34
replies
7.7k
views
15 follow
Forum: Do bioinformaticians often break molecular biologists' hearts by being the first author?
career authorship Forum
updated 7.3 years ago by ★ 4.6k • written 7.3 years ago by ▴ 650
145
votes
34
replies
51k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music cancer tcga mutation maf
updated 25 days ago by 38k • written 9.9 years ago by 5.9k
42
votes
33
replies
6.8k
views
8 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
meta how-to documentation
7 days ago by Ram 38k
68
votes
33
replies
15k
views
18 follow
Choosing Random Set Of Seqs From Larger Set
random fasta
updated 10 months ago by 38k • written 11.0 years ago by ▴ 190
50
votes
33
replies
47k
views
10 follow
I would like to add gene names to a volcano plot obtained from DEseq2
RNA-Seq DEseq2 R
updated 4.9 years ago by 84k • written 6.7 years ago by ▴ 320
12
votes
33
replies
2.0k
views
Missing sequences in local NT database
nt blast ncbi blastdbcmd
updated 4.5 years ago by 14k • written 4.5 years ago by ★ 2.6k
21
votes
33
replies
13k
views
high % of reads mapped to multiple loci after STAR mapping
RNA-Seq STAR single-end
updated 5.3 years ago by ▴ 970 • written 5.3 years ago by ★ 1.2k
11
votes
33
replies
16k
views
How we can analyze sanger sequence chromatogram?
SNP sequencing alignment sanger
updated 13 months ago by 38k • written 8.4 years ago by ▴ 40
48
votes
33
replies
41k
views
16 follow
Extract A Group Of Fasta Sequences From A File
fasta python perl biopython bioperl
updated 15 months ago by 38k • written 12.7 years ago by ▴ 60
127
votes
33
replies
53k
views
19 follow
VCF files: Change Chromosome Notation
vcf next-gen sequence
updated 4 months ago by 38k • written 8.9 years ago by ▴ 480
41
votes
33
replies
17k
views
10 follow
How To Convert Xml Into A Decent Parseable Format?
xml parsing perl subjective
updated 11.8 years ago by ▴ 30 • written 11.8 years ago by ★ 2.3k
143
votes
33
replies
27k
views
20 follow
C/C++ Libraries For Bioinformatics?
c c
updated 3.9 years ago by ▴ 50 • written 12.8 years ago by 13k
274
votes
33
replies
91k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 21 days ago by 38k • written 9.4 years ago by 20k
12
votes
33
replies
6.6k
views
9 follow
Back-filling missing genotypes in merged VCF
vcf
updated 3 months ago by 153k • written 8.4 years ago by ★ 1.0k
11
votes
33
replies
2.9k
views
Detect Regions In A List That Are Within 1 Megabase Of Each Other
python snp genomics overlap
updated 11.4 years ago by 52k • written 11.4 years ago by ▴ 350
10
votes
33
replies
2.6k
views
Looking for a tool like fastq screen but for ONT data
ont minion gridion tool nanopore
updated 4.7 years ago by 20k • written 4.7 years ago by ★ 1.4k
6
votes
33
replies
1.9k
views
I need to understand this image
phylogenies
updated 6.1 years ago by 23k • written 6.1 years ago by • 0
27
votes
33
replies
2.8k
views
7 follow
Forum: Biostars question catagories
biostars statistics Forum
6.4 years ago by John 13k
29
votes
33
replies
5.5k
views
12 follow
getBM error while using bioMart
biomart getBM ensembl
updated 2.4 years ago by • 0 • written 2.4 years ago by ▴ 160
24
votes
33
replies
7.3k
views
Contribute To The Nat Gen Paper "Principles For The Post-Gwas Functional Characterisation Of Risk Loci"
gwas snp
updated 12.3 years ago by 18k • written 12.3 years ago by 27k
129
votes
32
replies
121k
views
29 follow
Is There A Free Alternative To Ingenuity Pathway Analysis?
network pathway
updated 11 months ago by 38k • written 12.0 years ago by ▴ 530
153
votes
32
replies
7.0k
views
23 follow
Picking A Programming Language And Where To Begin
programming next-gen sequencing c subjective
updated 11.1 years ago by ▴ 60 • written 11.6 years ago by ★ 2.8k
82
votes
32
replies
6.4k
views
13 follow
Forum: Shall We Go Back To Stackexchange?
meta
updated 26 days ago by 38k • written 10.3 years ago by ★ 3.6k
53
votes
32
replies
11k
views
13 follow
Bio-Javascript?
updated 11 months ago by 38k • written 12.1 years ago by ★ 3.1k
10
votes
32
replies
2.8k
views
6 follow
Why my CD31+ endothelial cells RNAseq didn't express CD31?
CD31 HISAT2 endothelialcells Stringtie RNAseq
23 months ago by Youyy • 0
0
votes
32
replies
6.9k
views
DoHeatmap clusters, Seurat pipeline
scRNA-sequencing
2.5 years ago by Morris_Chair ▴ 330
3
votes
32
replies
2.4k
views
fastqc report for degradome reads
fastqc adaptor
5.0 years ago by Sam ▴ 150
93
votes
32
replies
30k
views
26 follow
Linux Distros Best Suited For Bioinformatics?
linux
written 11.1 years ago by ▴ 150
9
votes
32
replies
2.2k
views
Differentially gene expressed analyses of two different samples
RNA-Seq R next-gen rna-seq
updated 6.3 years ago by ▴ 600 • written 6.3 years ago by ▴ 790
88
votes
32
replies
8.2k
views
11 follow
Forum: Vintage / unconventional pictures for Bioinformatics
history picture
updated 12 months ago by 38k • written 8.4 years ago by 153k
32
votes
32
replies
6.9k
views
11 follow
Should We Be Using Much More Json In Our Delimited Data Formats?
gff vcf
updated 12.1 years ago by ★ 2.3k • written 12.1 years ago by ★ 3.2k
9
votes
31
replies
3.8k
views
6 follow
Clustering Million Points : Transcript Start And End Sites
clustering
updated 10.9 years ago by 18k • written 11.0 years ago by ★ 1.6k
46
votes
31
replies
15k
views
15 follow
Bwa Mem Have Different Alignment Result When Using Different Threads
updated 3.9 years ago by ★ 2.5k • written 9.2 years ago by ▴ 440
70
votes
31
replies
24k
views
10 follow
Illumina Instrument Type from fastq?
fastq
updated 7 months ago by 127k • written 6.7 years ago by 6.5k
96
votes
31
replies
96k
views
20 follow
How To Split A Bam File By Chromosome
bam split chromosome
updated 12 months ago by ▴ 70 • written 10.8 years ago by ▴ 390
11
votes
31
replies
5.9k
views
Using wildcards to accept paired-end reads from Snakemake
snakemake WGS
2.8 years ago by moldach686 ▴ 80
7
votes
31
replies
13k
views
Scale and Center [normalized] RNA-seq expression counts for PCA ?
sequencing pca genome R RNA-Seq
updated 10 months ago by 38k • written 8.1 years ago by ▴ 250
118
votes
31
replies
174k
views
17 follow
Correct Way To Parse A Fasta File In Python
fasta parsing python
updated 17 months ago by 127k • written 12.9 years ago by 11k
14
votes
31
replies
3.7k
views
9 follow
make fasta sequence which is multiple of three
alignment
4.9 years ago by alim.hcu ▴ 20
30
votes
31
replies
2.6k
views
11 follow
Forum: I need your help to find my future
future master company student internship Forum
updated 6.6 years ago by ★ 1.4k • written 6.7 years ago by ▴ 90
10
votes
31
replies
3.2k
views
7 follow
Extract columns from a vcf file using identifiers from a second file
snp
updated 16 months ago by 127k • written 4.9 years ago by ▴ 20
53
votes
31
replies
5.3k
views
15 follow
Biostar Flyer For Outreach
biostars
updated 5 weeks ago by 38k • written 12.4 years ago by 11k
99
votes
31
replies
81k
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
59
votes
31
replies
3.4k
views
12 follow
News: Example of how bioinformaticians can publish in Scientific Reports (by nature publishing group) using publicly available NGS data
publication NGS News
updated 6.2 years ago by ▴ 50 • written 6.2 years ago by 9.9k
78
votes
31
replies
5.7k
views
14 follow
Forum: Do Bad Questions Even Exist?
biostars general education
updated 5 weeks ago by 38k • written 12.1 years ago by 10k
12
votes
31
replies
4.7k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
geneset genome gene abinitio
updated 12 days ago by 38k • written 3.6 years ago by 7.7k
1,000 results • Page 5 of 20
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Gene Set Enrichment Analysis
Can I sort my bam files with Picard MergeSamFiles?
Answer: Problem generating a .vcf after upgrade of samtools and bcftools
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Recent Replies
Answer: How to implement this two-stage one-to-many workflow using WDL? by Ruben • 0
> Unfortunately, as far as I can tell, WDL provides no support for iterating over the contents of a directory. (I find this shocking. I con…
Answer: activity of unloaded/unassembled Tn5 by callumjcparr • 0
So I hope someone is still interested in this. We have taken to preparing recombinant Tn5 now as it's much cheaper than commercial suppli…
Comment: RNA-SEQ by ali • 0
thanks for your helping
Comment: TSS of protein coding genes by ConvolutedGenome ▴ 10
I am quite confused with GENCODE GTF file, So, within the GENCODE GTF file, I noticed that each (protein-coding) gene has multiple "transc…
Comment: Recommendation for (Alternative) Splicing analysis packages for bulk RNA-seq da by iraun 5.8k
Hi! I personally use [SplAdder][1], in case you want to add it to your list :). [1]: https://github.com/ratschlab/spladder
Answer: Problem generating a .vcf after upgrade of samtools and bcftools by Andy • 0
Really the only needed, that help worked, thank's
Comment: Active enhancers for mm39 by seidel 11k
Just curious what you mean by "active" enhancers. Enhancers are active in a given context (e.g. cell type developmental state, etc.), and m…
Comment: Creating loop for read groups using Picard by ntsopoul ▴ 20
try absolute paths navigate to the directory with cd and use pwd to get the absolute directory.
Comment: how to create interacting Hi-C peaks by rheab1230 ▴ 140
Thank you. I will use this package since I am more familiar with R
Comment: how to create interacting Hi-C peaks by rheab1230 ▴ 140
thank you. i will go through it
Comment: Fastqc report analysis by npavliukovec • 0
Yeah, after trimming and fastqc I will have to generate MultiQC plots and after do mapping with reference genome. As I know, for eukaryotes…
Comment: My fastq files(paired end) have different read number by kimgeng • 0
Oh, I see, Thank you however, I want to make vcf files with gatk haplotypecaller and GenotypeGVCFs. But I got some problems I have about 2.…
Answer: My fastq files(paired end) have different read number by ntsopoul ▴ 20
Yes, this is normal because depending on how you generate the bam file, the non-aligning reads are saved in the .bam file along the properl…
Answer: Can I use abundance from Tximport to compare the expression level of transcript by ntsopoul ▴ 20
No, you should not do that since the count matrix is not normalized. Also, the statistics for getting a pValue requires consideration of al…
Comment: Easy way to split VCF file by chromosome by Joana • 0
You need to run bcftools index on your vcf file before running the suggested command.
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