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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
6.2k
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 8 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
6.7 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
7
replies
903
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
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
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
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 4.2 years ago by ▴ 470
17
votes
19
replies
2.2k
views
Sorting sequences according header
software error sequence Assembly next-gen
6.8 years ago by Gian77 ▴ 60
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
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
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
17
replies
2.7k
views
6 follow
RNA seq pipeline
RNA-Seq
5.6 years ago by dimitrischat ▴ 180
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
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
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 2.4 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
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
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
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
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
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
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
2.4k
views
7 follow
SAM / BAM alignments
SAM BAM
6.4 years ago by John 13k
12
votes
10
replies
3.7k
views
Speed up BLASTp vs NCBI nr database
blast
7.0 years ago by biotech ▴ 570
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
11
replies
2.8k
views
How To Get Snp Genotypes
snp genotyping
updated 11.8 years ago by 11k • written 12.1 years ago by ▴ 20
1,000 results • Page 1 of 20
Recent Votes
Comment: Low mapping percentage
Comment: Low mapping percentage
A: genomicranges outside sequence bounds
A: how can i download human ribosomal reference ?
Bayesian network for biological data using bnlearn
Comment: What does canonical transcript mean in the context of VEP
Answer: What does canonical transcript mean in the context of VEP
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Recent Replies
Comment: Low mapping percentage by Sib ▴ 40
Thank you for the reply. If there is not much I can do about the contamination at this stage, what is the benefit of knowing the source of…
Answer: integrate single cell RNA sequencing data by Hamid Ghaedi 2.9k
There are different approaches that you may choose to deal with batch correction. Harmony is one of those approaches that has been shown to…
Comment: What does canonical transcript mean in the context of VEP by Vincent Laufer ★ 2.9k
@curious - The only thing I have to add to @yokofakun 's precise answer is that, while you are considering and reading about Ensembl canoni…
Comment: Help with running ATAC using Encode pipeline by Chris ▴ 100
Thank you for the instruction! I see the beside json file we also have input file which I am confused. Because we have already defined the …
Comment: Comparing loci across catalogs by rycro_c • 0
Hi @Austin, Did you ever figure this out?
Comment: Low mapping percentage by Dave Carlson ★ 1.3k
I've been faced with similar issues in the past. Both option 1 and 2 seem useful. You can also treat your data as accidental metagenomic …
Comment: How to sort gff3 according to chromosome order? by Pierre Lindenbaum 154k
-s, --stable stabilize sort by disabling last-resort comparison
Comment: Low mapping percentage by GenoMax 129k
If you do have contamination (either from rRNA of same species or from true contaminant(s)) there is not much you can do about that at this…
Comment: Optimum setting for local blastp for ~10K sequences by GenoMax 129k
> Running the same sequence on the blast web server took 10 seconds Don't try to compare anything local with NCBI's web blast infrastruct…
Comment: how to Construct a Newick tree file from five large fasta files by Joe 21k
Yes, I know - but that doesn't answer the question. **What *kind* of phylogenetic tree?**
Comment: Optimum setting for local blastp for ~10K sequences by sodiumnitrate ▴ 20
Thank you for the explanation! I managed to get diamond to work, but I'm having trouble getting it to run faster than blast. For a single t…
Comment: What is "pident" (percentage of identical matches) in the "Diamond" protein alig by GenoMax 129k
That is the question @Vincent answer poses since it seems to correspond to something different. You can also create an issue on https://gi…
Answer: How to sort gff3 according to chromosome order? by GenoMax 129k
Please use `AGAT`: https://agat.readthedocs.io/en/latest/topological-sorting-of-gff-features.html
Comment: convert data frame with character column to data frame with integer column by atemedorri137798 • 0
dear @Basti : As you said in order to clarify my issue I edit question box with give an example. I will be grateful if you take a look at …
Comment: How to sort gff3 according to chromosome order? by Ram 39k
Those are your options with the `sort` utility - you can either keep the existing order or re-order by coordinate. If you're looking for a …
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