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1,000 results • Page 4 of 20
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87
votes
37
replies
50k
views
20 follow
Venn/Euler Diagram Of Four Or More Sets
r
updated 21 months ago by 41k • written 10.4 years ago by ▴ 110
34
votes
37
replies
16k
views
6 follow
How to cluster genes in heatmap
RNA-Seq R gene
updated 6.0 years ago by 41k • written 6.0 years ago by ▴ 820
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
43
votes
37
replies
2.2k
views
7 follow
Forum: Checking the quality and reliability in bioinformatics
reproducibility
updated 6 months ago by 41k • written 6.1 years ago by ★ 4.2k
16
votes
37
replies
16k
views
7 follow
extracting the soft clipped seq only from a sam file
sam bam soft clip
updated 7.4 years ago by 20 • written 8.9 years ago by ★ 1.3k
17
votes
37
replies
4.2k
views
No alias or index file found for protein database
next-gen software error sequence
updated 4.5 years ago by 20 • written 4.6 years ago by ▴ 500
130
votes
37
replies
13k
views
27 follow
What Are The Obsolete Research Topics In Bioinformatics?
updated 12.2 years ago by ★ 1.3k • written 12.2 years ago by ▴ 820
18
votes
37
replies
13k
views
11 follow
Is it possible to download the full EpiCov database from GISAID?
GISAID genome Database EpiCoV
updated 2.6 years ago by ▴ 270 • written 3.7 years ago by ▴ 30
5
votes
37
replies
3.1k
views
search text in one file and then replace with text from another file
search replace multiple files
6.1 years ago by mforthman ▴ 40
244
votes
36
replies
8.9k
views
32 follow
Forum: Good Habit for Bioinformatics Analyst or Scientist
Analyst Scientist
updated 7 months ago by 41k • written 7.6 years ago by ★ 9.3k
49
votes
36
replies
8.2k
views
11 follow
Forum: New features and bug fixes for Biostar to work on during Google Summer of Code
meta biostars gsoc
updated 9 months ago by 41k • written 9.6 years ago by ▴ 110
36
votes
36
replies
36k
views
17 follow
Fetching Genbank Entries For List Of Accession Numbers.
ncbi entrez
updated 2.5 years ago by • 0 • written 10.7 years ago by ▴ 140
11
votes
36
replies
33k
views
6 follow
python script error: ImportError: No module named pysam
pysam pythonscript .py overlapsignature
updated 5.5 years ago by ★ 2.1k • written 5.5 years ago by ▴ 110
10
votes
36
replies
5.3k
views
Design in DESeq: Can you combine explicit and implicit batch effect correction in (SVA+Metadata Variables)?
DESeq2 R batch effects SVA
updated 5.2 years ago by ▴ 20 • written 5.3 years ago by ▴ 620
40
votes
36
replies
13k
views
9 follow
Obtaining uniquely mapped reads from BWA mem alignment (filtering by q score does not seem to do the trick in my case)
next-gen alignment bwa
updated 6.5 years ago by 13k • written 6.5 years ago by ▴ 130
18
votes
36
replies
4.0k
views
6 follow
GPL6883_HumanRef-8_V3_0_R0_11282963_A (illumina expression beadchip)
R
updated 12 months ago by ★ 1.8k • written 3.0 years ago by ▴ 70
59
votes
36
replies
37k
views
27 follow
Pca From Vcf Files
pca genome vcf
updated 16 months ago by ▴ 40 • written 11.6 years ago by ▴ 830
3
votes
36
replies
4.6k
views
inquiry related to snpsift
rsid snp vcf
updated 2.3 years ago by 86k • written 2.4 years ago by ▴ 140
251
votes
36
replies
32k
views
27 follow
Forum: How Do You Manage Your Files & Directories For Your Projects ?
project-management file-management
updated 8 months ago by 41k • written 13.6 years ago by 158k
38
votes
36
replies
5.8k
views
11 follow
Largest Bioinformatics Software Project?
software comparison
updated 12.7 years ago by 33k • written 12.7 years ago by ▴ 40
84
votes
36
replies
18k
views
13 follow
Forum: Benchmark - Comparison of Different NGS Mappers
mRNA-Seq benchmark NGS-mapper
updated 20 months ago by 41k • written 8.9 years ago by 10k
9
votes
36
replies
11k
views
18 follow
Convert Gene IDs of Tomato Sol Database
tomato gene
updated 12 months ago by 41k • written 8.4 years ago by ▴ 170
16
votes
36
replies
6.5k
views
Automating Trimmomatic for total Noobs
RNA-Seq
updated 4.8 years ago by 99k • written 4.8 years ago by ▴ 30
25
votes
36
replies
12k
views
13 follow
ATAC-seq DE analysis
ATAC-seq Differential expression
updated 2.6 years ago by • 0 • written 5.5 years ago by ▴ 40
88
votes
36
replies
38k
views
15 follow
1000 Genomes Ld Calculation
genome linkage gwas
updated 9.8 years ago by ▴ 970 • written 13.1 years ago by ★ 3.4k
34
votes
35
replies
15k
views
8 follow
Sample names for TCGA data from GDC-legacy archive
RNA-Seq tcga gdc
updated 4.7 years ago by ▴ 30 • written 5.7 years ago by ▴ 740
149
votes
35
replies
61k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 9 months ago by 41k • written 11.0 years ago by ★ 1.6k
56
votes
35
replies
13k
views
9 follow
How to get sample names and genotype for SNP in multi-sample VCF file
SNP genotype GATK
updated 8 weeks ago by 86k • written 5.8 years ago by ▴ 520
2
votes
35
replies
10k
views
BWA-MEM using long PacBio reads
PacBio alignement bwa-mem sam
updated 6.9 years ago by 19k • written 6.9 years ago by ★ 1.4k
26
votes
35
replies
31k
views
16 follow
Calculate The Frequency Of Nucleotides At Each Position In An Mpileup File
mpileup
updated 10 months ago by ▴ 10 • written 9.7 years ago by ★ 4.1k
17
votes
35
replies
3.2k
views
reading blast result file
blast
7.0 years ago by nasromer2191989 ▴ 20
121
votes
35
replies
41k
views
20 follow
Forum: Snakemake vs. Nextflow: strengths and weaknesses
snakemake nextflow
updated 6 months ago by 41k • written 6.5 years ago by ▴ 810
76
votes
35
replies
29k
views
13 follow
Illumina Instrument Type from fastq?
fastq
updated 7 months ago by ▴ 20 • written 7.4 years ago by 6.5k
45
votes
35
replies
5.5k
views
12 follow
Forum: looking for a bioinformatics project to do during military rotation
military
updated 17 months ago by 41k • written 6.2 years ago by ▴ 60
5
votes
35
replies
3.0k
views
Reduce set of chromosomes in Pangenome graph
pangenome vg
updated 4 months ago by ▴ 410 • written 5 months ago by • 0
22
votes
35
replies
5.4k
views
Removing identifier with "unavailable sequence" from FASTA file
sequence genome blast RNA-Seq
updated 20 months ago by 41k • written 8.9 years ago by ★ 1.8k
40
votes
35
replies
12k
views
10 follow
find positions of a short sequence in a genome
sequence search
updated 3 months ago by ★ 1.5k • written 7.3 years ago by 13k
14
votes
35
replies
9.2k
views
8 follow
Converting large (compressed and unsorted) BAM files to fastq
BAM fatsq alignment bedtools picard
updated 2.3 years ago by 136k • written 7.0 years ago by ▴ 580
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
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
79
votes
35
replies
8.9k
views
17 follow
Forum: Do bioinformaticians often break molecular biologists' hearts by being the first author?
authorship career
updated 6 months ago by • 0 • written 8.0 years ago by ▴ 650
65
votes
35
replies
20k
views
17 follow
Which Dna Compression Algorithms Are Actually Used?
dna
updated 15 months ago by 158k • written 12.5 years ago by ▴ 270
15
votes
35
replies
3.1k
views
To obtain upstream DNA sequence by giving location
SNP R genome
updated 5.0 years ago by 78k • written 5.0 years ago by ▴ 150
4
votes
35
replies
9.0k
views
Is They Any Software Or Technique To Find The Number Of Reads Mapped To Each Contig After Aligment
mapping RNA-seq
updated 9 months ago by 41k • written 9.9 years ago by ▴ 50
83
votes
34
replies
17k
views
22 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment R pathway active-subnetwork
updated 6 months ago by • 0 • written 5.4 years ago by ★ 1.3k
32
votes
34
replies
15k
views
10 follow
How To Randomly Sample A Subset Of Lines From A Bed File
bed chip-seq
updated 2.1 years ago by 41k • written 10.1 years ago by ▴ 540
80
votes
34
replies
4.7k
views
11 follow
Forum: Authorship issues- how to resolve?
authorship
updated 11 months ago by 41k • written 8.5 years ago by ▴ 520
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
43
votes
34
replies
12k
views
7 follow
Technical replicates in RNAseq
RNA-Seq technical_replicates
21 months ago by grant.hovhannisyan ★ 2.6k
2
votes
34
replies
6.3k
views
How to install pip on HPC server
software error
5.8 years ago by Bioinfonext ▴ 440
1,000 results • Page 4 of 20
Recent Votes
Answer: GO categorization
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
Answer: GO categorization
C: Expected a file with 2 fields per line. GenomicsDBImport from GATK ?
C: Expected a file with 2 fields per line. GenomicsDBImport from GATK ?
Answer: Problematic fastq files...How can we trust them?
Comment: Problematic fastq files...How can we trust them?
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Popular Question to beausoleilmo ▴ 560
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Recent Replies
Answer: "MethylKit" package for WGBS data by viveksomya123 • 0
Why I am getting this histogram of CpG coverage using methylkit, is this the failure of bisulfite library preparation![enter image descript…
Comment: Should I scale all genes in single cell Seurat? by synat.keam ▴ 80
Thanks, António for your kind and detailed responses. You helped clear my doubt about scaling! Kind Regards, Synat
Comment: Using metagenome assembly and binning to identify and mitigate contamination in by Brian Bushnell 19k
It's not a silly question! And yes, it can be done. JGI is currently testing various binning tools to try to find the best protocol for t…
Answer: GO categorization by geneontologyhelp ▴ 270
[We have this in our FAQ][1]. PANTHER version 18.0, which powers the enrichment analysis on our homepage, has [143 species][2] loaded and …
Comment: Problematic fastq files...How can we trust them? by blackadder ▴ 30
Thanks for the feedback fellas! I agree with the aforementioned!
Comment: Which program, tool, or strategy do you use to visualize genomic rearrangements? by cmdcolin ★ 3.4k
i collect a large list of tools for visualization, some are specialized for SVs and re-arrangements. you can filter by tag (SV, CNV, compar…
Answer: The number of variations in the pan-genome is reduced compared to the variations by Jordan M Eizenga ▴ 410
If variants overlap in the genome, `vg deconstruct` will combine them into one locus with multiple alleles. If your input VCF has a lot of …
Answer: How to find node Postion and source(sample) ? by Jordan M Eizenga ▴ 410
You can use `vg find -P` for this. This command is not really designed to be used frequently throughout the genome (each invocation loads t…
Comment: How Can I move the scattered dots more closer into the center of box ? by Brian Bushnell 19k
I would just draw them in by hand where you want them.
Comment: How to identify CG, CHG, or CHH from MeDIP data by Tm ★ 1.1k
I know that CpG types can be identified using whole genome bisulphite data. But could it be possible using MeDIP data too? We tried using Q…
Comment: Problematic fastq files...How can we trust them? by Brian Bushnell 19k
I'd have to agree there... while you can generally recover a fastq to the point that it is spec-compliant, you don't know how or why the f…
Answer: Finding human .vcf files online to download by cmdcolin ★ 3.4k
---------- some common ones include 1000 genomes vcf (large, multi-sample) http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ …
Comment: GO categorization by m.habib • 0
Thanks Istvan for your reply. I think these programs will do the same as Trinotate. Trinotate searches against numerous databases and gener…
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp by jv ★ 1.2k
I wonder if using cell hashing, which would allow pooling of cells from multiple samples before droplet formation, could improve things her…
Comment: Where Can I Find The Basepair Positions Of Chromosome Bands? by Malachi Griffith 19k
And the hg38 version can be found here: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/cytoBand.txt.gz And for convenience, upda…
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