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41
votes
55
replies
10k
views
6 follow
hash function for DNA sequences
hash hashing DNA
7.2 years ago by midox ▴ 290
27
votes
17
replies
17k
views
12 follow
Dotplot for filtered pathways result
pathways ggplot2 clusterProfiler r dotplot
18 months ago by Leite ★ 1.2k
24
votes
25
replies
6.1k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq beta diversity metagenomics
2.8 years ago by dpc ▴ 240
23
votes
22
replies
40k
views
6 follow
Converting VCF to PLINK .bed binary fileset to check for pedigree errors with KING: How do conversion tools make the PLINK .fam file, without asking …
plink vcf fam gatk vcftools
updated 6 months ago by • 0 • written 5.1 years ago by ▴ 250
23
votes
10
replies
5.1k
views
How to predict individual ethnicity information by using hapmap data
SNP Ethnicity Hapmap
updated 2.1 years ago by 85k • written 5.3 years ago by ▴ 40
22
votes
20
replies
2.1k
views
what is the prefered strategy to treat with blast-less transcriptomes from RNA-seq
blast RNA-Seq genome gene
updated 7 weeks ago by 39k • written 6.9 years ago by ★ 3.4k
22
votes
19
replies
2.5k
views
targets of a list of miRNAs
miRNAs RNA-Seq DEanalysis target-prediction
6.6 years ago by fi1d18 ★ 4.2k
20
votes
17
replies
5.2k
views
HiSeq 4000 PhiX screening and removal using bbduk
spikein filtering bbmap bbduk phix
5.8 years ago by Anand Rao ▴ 560
20
votes
15
replies
26k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink SNP
updated 10 months ago by 39k • written 7.4 years ago by ▴ 190
19
votes
43
replies
4.2k
views
Annotation of huge number of CNV files
CNV annotation TCGA
4.8 years ago by nazaninhoseinkhan ▴ 510
18
votes
4
replies
8.2k
views
How To Find Rna-Seq Data Of Published Papers?
geo next-gen RNA-seq
updated 3 months ago by 39k • written 9.8 years ago by ▴ 930
18
votes
19
replies
1.7k
views
6 follow
Extremely important marker gene has many reads based on IGV viewer but no quantified reads
rna-seq sequencing igv alignment next-gen
updated 6 months ago by 39k • written 4.4 years ago by • 0
18
votes
7
replies
901
views
How to calculate if statistically a variable of a bulk RNA-seq affects the comparison of interest?
DESeq2 Variable RNA-seq
8 months ago by Rafael Soler ★ 1.2k
17
votes
19
replies
2.2k
views
Sorting sequences according header
software error sequence Assembly next-gen
6.8 years ago by Gian77 ▴ 60
17
votes
8
replies
1.9k
views
Number of unique authors in PubMed in last 10 years
PubMed
7.2 years ago by nejc ▴ 50
17
votes
37
replies
3.5k
views
No alias or index file found for protein database
next-gen software error sequence
updated 4.0 years ago by 20 • written 4.1 years ago by ▴ 470
17
votes
13
replies
5.6k
views
7 follow
BWA: Why paired reads mapped to different chromosome?
alignment genome sequencing
6.0 years ago by lghust2011 ▴ 100
16
votes
18
replies
4.1k
views
8 follow
Python Program to read .fasta file to .txt file
Python
updated 3.8 years ago by ★ 23k • written 3.8 years ago by • 0
16
votes
21
replies
1.6k
views
Why there are different hit for a same gene in different species
gene blast ortholog paralog
6.7 years ago by Farbod ★ 3.4k
16
votes
17
replies
2.7k
views
6 follow
RNA seq pipeline
RNA-Seq
5.6 years ago by dimitrischat ▴ 180
16
votes
38
replies
16k
views
Differential gene Analysis by Limma
Limma Microarray R
updated 13 months ago by 39k • written 8.3 years ago by ▴ 920
16
votes
10
replies
4.9k
views
6 follow
Powerful desktop computer for genomics
next-gen sequencing ChIP-Seq RNA-Seq
7.0 years ago by Alternative ▴ 270
16
votes
16
replies
2.5k
views
Using DESeq2 results for building a classifier
deseq2 RNA-Seq differentially expressed genes
5.2 years ago by bioinfo456 ▴ 150
16
votes
8
replies
1.7k
views
8 follow
What are the most important unresolved problems in Bioinformatics?
bioinformatics
updated 7 weeks ago by 39k • written 6.7 years ago by ★ 2.4k
16
votes
14
replies
14k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters trimmomatic RNA-seq
4.9 years ago by salamandra ▴ 540
15
votes
14
replies
2.4k
views
Penalty model of BWA MEM and BOWTIE2?
RNA-Seq bwa mem bowtie2 alignment
5.4 years ago by John ▴ 270
15
votes
14
replies
1.5k
views
how can interpret these biologically weird results?
RNA-Seq
updated 2.3 years ago by 20 • written 5.6 years ago by ▴ 330
15
votes
19
replies
1.4k
views
trimmomaric command for a fasta file?
trimmomatic
updated 5.1 years ago by 39k • written 5.1 years ago by • 0
14
votes
8
replies
4.6k
views
Unable To Replicate Splice Junction In Tophat
tophat2 bam
9.6 years ago by Dan D 7.4k
14
votes
30
replies
2.6k
views
Download GTF/GFF annotation data for NT database, not by organism (for STAR alignment)
RNA-Seq rna-seq alignment next-gen
4.1 years ago by Malka ▴ 70
14
votes
18
replies
4.2k
views
GATK Haplotype Caller
next-gen GATK haplotype caller contigs
updated 6.4 years ago by 20 • written 6.6 years ago by ▴ 50
14
votes
16
replies
1.4k
views
Why are some mapped reads not mapped completely?
RNA-Seq mapping
updated 2.6 years ago by 14k • written 2.6 years ago by ▴ 80
14
votes
5
replies
2.8k
views
bioinformatics basic training
genome
updated 11 weeks ago by 39k • written 8.5 years ago by • 0
13
votes
7
replies
5.9k
views
Why some probes have "NA" for gene symbol and Entrez ID?
affymetrix microarray NA genesymbol
updated 6.5 years ago by 20 • written 6.5 years ago by ▴ 250
13
votes
13
replies
13k
views
How to interpret Per sequence GC content module in FastQC for RNA-seq data?
RNA-Seq FastQC QC GC-content
3.8 years ago by Arindam Ghosh ▴ 500
13
votes
11
replies
5.7k
views
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
RNA-Seq QC
4.6 years ago by jackgrayner ▴ 80
13
votes
13
replies
1.1k
views
Is reproducibility of identified variants in a gene important in Sanger sequencing?
reproducibility sanger sequencing variants
3.6 years ago by DanielC ▴ 160
13
votes
6
replies
10k
views
6 follow
MAF vs VAF
sequencing
5.2 years ago by lauren.wahyudi ▴ 40
13
votes
22
replies
9.2k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva combat batch effects
updated 5.7 years ago by 20 • written 5.9 years ago by ★ 1.3k
13
votes
16
replies
5.7k
views
6 follow
Confused about how to generate a consensus sequence after bwa
bwa samtools mpileup
4.4 years ago by DNAngel ▴ 240
13
votes
16
replies
5.1k
views
Mask or trim primer sequences in Amplicon sequencing
amplicon mask trimming fastq
6.4 years ago by Paul ★ 1.5k
13
votes
24
replies
3.5k
views
Error of bam-to-sam conversion using samtools
samtools TopHat2 RNA-Seq BAM SAM
updated 6.2 years ago by 129k • written 6.2 years ago by ▴ 480
13
votes
13
replies
8.0k
views
How to do pca plot from .eigenval and .eigenvec files from Plink in R.
R SNP
updated 5.2 years ago by 103k • written 5.2 years ago by ▴ 70
13
votes
19
replies
4.5k
views
bbmerge not joining paired-end reads
bbmerge alignment
5.5 years ago by bioplanet ▴ 60
12
votes
28
replies
1.9k
views
Calculating the expression level of genes
Gene expression RNA-Seq R
5.0 years ago by Za ▴ 140
12
votes
10
replies
2.4k
views
7 follow
SAM / BAM alignments
SAM BAM
6.4 years ago by John 13k
12
votes
14
replies
4.6k
views
bedtools intersect error?
ChIP-Seq bedtools intersect
4.3 years ago by star ▴ 340
12
votes
17
replies
4.0k
views
How do I generate all possible Newick Tree permutations for a set of species given an outgroup in Python?
Python Newick phylogenetics tree phylogeny
5.6 years ago by anonymous1192976466 ▴ 50
12
votes
10
replies
3.7k
views
Speed up BLASTp vs NCBI nr database
blast
7.0 years ago by biotech ▴ 570
12
votes
11
replies
2.8k
views
How To Get Snp Genotypes
snp genotyping
updated 11.7 years ago by 11k • written 12.1 years ago by ▴ 20
1,000 results • Page 1 of 20
Recent Votes
Problem with PGDSpider v 2.1.0.2
Comment: Filter VCF file for variant alleles
Help making ADMIXTURE output digestible
Answer: Graphing Average Expression of Group of Genes
Linear models with limma: coefficients not estimatable, are the others OK?
Answer: How to find gene annotation given a position in a bacterial genome
Comment: INSTALLING DEseq2 via conda
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Recent Replies
Comment: how to run FacetsSuite wrapper scripts on command line by Dalal • 0
This is the code I ran: Rscript --vanilla snp-pileup-wrapper.R --snp-pileup-path ~/mut_analysis/variant-calling/facets_cnv/ --vcf-file ~/mu…
Answer: Michigan Imputation Server - Local docker image by Vincent Laufer ★ 2.8k
Hi Ms. or Mr. Effect, A couple ideas: 1) if its not working on the local docker image, have you tried uploading your data for imputat…
Answer: Manhattan Plot with independent significant hits by Vincent Laufer ★ 2.8k
Consider using [locuszoom][1] for genomic regions small enough to warrant special clarification that the two associations are independent. …
Comment: Problem with PGDSpider v 2.1.0.2 by sackettl ▴ 20
I have this same problem with version 2.1.1.5. Did you ever find a solution?
Comment: Filter VCF file for variant alleles by Ram 39k
> can't find anything to do this It's in there. If you had looked a little deeper, you would have found - on your own - exactly what Pierr…
Comment: To call variants can I use my aligned WGS data as a reference genome by GenoMax 129k
Then create an alternate Reference with data for the sample: https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateR…
Comment: Help making ADMIXTURE output digestible by Aaron ▴ 10
You can also check out [pong][1] (README [here][2]), which creates interactive plots with the clusters and colors automatically aligned acr…
Comment: To call variants can I use my aligned WGS data as a reference genome by mls • 0
Yes they are but I wanna compare one of my samples with others , rather S288C.
Comment: To call variants can I use my aligned WGS data as a reference genome by Pierre Lindenbaum 154k
the bam are mapped on S288C fasta isn't it ? why would you need another reference ?
Comment: Filter VCF file for variant alleles by Pierre Lindenbaum 154k
use a filtering expression https://samtools.github.io/bcftools/bcftools.html#expressions , something like; bcftools view -i 'COUNT(GT=…
Comment: Filter VCF file for variant alleles by miguellarrazlopezdenovales • 0
I've tried bcftools, which seems to be the closest I've got, but I can't find anything to do this. I have also found vcftools --max-non-ref…
Comment: Filter VCF file for variant alleles by Ram 39k
What have you tried? You've mentioned bcftools as a tag, have you read the manual?
Comment: How to concatenate multiple fasta file by doggie • 0
@shenwei356 Thank you so much! Your prompt reply helped me a lot!
Answer: PacBio Pipeline and Tools for Variant Call by William Rowell ▴ 250
> What are Quality parameters that should be taken care ( Adapter trim, Reads filter, Min Data size, ) How to trim adapter, What tools to u…
Comment: Ambient RNA expression correction by rpolicastro 12k
Ambient RNA would have the same cell barcode as a valid cell-containing droplet since the RNA gets partitioned into the droplet with the ce…
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