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41
votes
55
replies
8.9k
views
6 follow
hash function for DNA sequences
hash hashing DNA
6.4 years ago by midox ▴ 290
27
votes
17
replies
14k
views
12 follow
Dotplot for filtered pathways result
pathways ggplot2 clusterProfiler r dotplot
8 months ago by Leite ★ 1.2k
24
votes
25
replies
4.5k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq beta diversity metagenomics
2.1 years ago by dpc ▴ 240
23
votes
21
replies
31k
views
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
4.3 years ago by gaelgarcia ▴ 250
23
votes
10
replies
4.7k
views
How to predict individual ethnicity information by using hapmap data
SNP Ethnicity Hapmap
updated 16 months ago by 82k • written 4.5 years ago by ▴ 40
22
votes
20
replies
1.8k
views
what is the prefered strategy to treat with blast-less transcriptomes from RNA-seq
RNA-Seq blast gene genome Forum
6.1 years ago by Farbod ★ 3.3k
22
votes
19
replies
2.2k
views
targets of a list of miRNAs
miRNAs RNA-Seq DEanalysis target-prediction
5.9 years ago by Angel ★ 4.1k
19
votes
43
replies
3.5k
views
Annotation of huge number of CNV files
CNV annotation TCGA
4.0 years ago by nazaninhoseinkhan ▴ 430
18
votes
4
replies
7.7k
views
How To Find Rna-Seq Data Of Published Papers?
bioinformatics next-gen rna-seq geo
9.0 years ago by user ▴ 870
18
votes
19
replies
1.4k
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
3.6 years ago by rbkh09 • 0
17
votes
8
replies
1.6k
views
Number of unique authors in PubMed in last 10 years
PubMed
6.4 years ago by nejc ▴ 50
17
votes
13
replies
4.8k
views
7 follow
BWA: Why paired reads mapped to different chromosome?
alignment genome sequencing
5.3 years ago by lghust2011 ▴ 100
17
votes
37
replies
2.8k
views
No alias or index file found for protein database
next-gen software error sequence
updated 3.2 years ago by 20 • written 3.4 years ago by ▴ 430
17
votes
19
replies
1.8k
views
Sorting sequences according header
software error sequence Assembly next-gen
6.0 years ago by Gian77 ▴ 60
16
votes
21
replies
1.3k
views
Why there are different hit for a same gene in different species
gene blast ortholog paralog
5.9 years ago by Farbod ★ 3.3k
16
votes
18
replies
2.7k
views
8 follow
Python Program to read .fasta file to .txt file
Python
updated 3.0 years ago by ★ 20k • written 3.0 years ago by • 0
16
votes
14
replies
12k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters trimmomatic RNA-seq
4.1 years ago by salamandra ▴ 500
16
votes
10
replies
4.4k
views
6 follow
Powerful desktop computer for genomics
next-gen sequencing ChIP-Seq RNA-Seq
6.2 years ago by Alternative ▴ 270
16
votes
8
replies
1.5k
views
8 follow
What are the most important unresolved problems in Bioinformatics?
problem unresolved bioinformatics
updated 5.8 years ago by 20 • written 5.9 years ago by ★ 2.4k
16
votes
38
replies
15k
views
Differential gene Analysis by Limma
Limma Microarray R
updated 3 months ago by 36k • written 7.5 years ago by ▴ 920
16
votes
16
replies
2.1k
views
Using DESeq2 results for building a classifier
deseq2 RNA-Seq differentially expressed genes
4.4 years ago by Uday Rangaswamy ▴ 150
16
votes
17
replies
2.4k
views
6 follow
RNA seq pipeline
RNA-Seq
4.8 years ago by dimitrischat ▴ 180
15
votes
14
replies
1.9k
views
Penalty model of BWA MEM and BOWTIE2?
RNA-Seq bwa mem bowtie2 alignment
4.6 years ago by John ▴ 240
15
votes
15
replies
23k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink SNP
updated 16 days ago by 36k • written 6.6 years ago by ▴ 180
15
votes
19
replies
1.1k
views
trimmomaric command for a fasta file?
trimmomatic
updated 4.3 years ago by 36k • written 4.3 years ago by • 0
15
votes
14
replies
1.2k
views
how can interpret these biologically weird results?
RNA-Seq
updated 19 months ago by 20 • written 4.8 years ago by ▴ 320
14
votes
17
replies
4.5k
views
HiSeq 4000 PhiX screening and removal using bbduk
spikein filtering bbmap bbduk phix
5.0 years ago by Anand Rao ▴ 520
14
votes
8
replies
4.4k
views
Unable To Replicate Splice Junction In Tophat
tophat2 bam
8.9 years ago by Dan D 7.3k
14
votes
5
replies
2.5k
views
bioinformatics basic training
genome Tutorial
updated 5 months ago by 36k • written 7.7 years ago by • 0
14
votes
16
replies
1.0k
views
Why are some mapped reads not mapped completely?
RNA-Seq mapping
updated 21 months ago by 14k • written 21 months ago by ▴ 80
14
votes
18
replies
3.8k
views
GATK Haplotype Caller
next-gen GATK haplotype caller contigs
updated 5.6 years ago by 20 • written 5.8 years ago by ▴ 50
14
votes
30
replies
2.1k
views
Download GTF/GFF annotation data for NT database, not by organism (for STAR alignment)
RNA-Seq rna-seq alignment next-gen
3.3 years ago by Malka ▴ 70
13
votes
7
replies
5.3k
views
Why some probes have "NA" for gene symbol and Entrez ID?
affymetrix microarray NA genesymbol
updated 5.7 years ago by 20 • written 5.8 years ago by ▴ 230
13
votes
13
replies
7.3k
views
How to do pca plot from .eigenval and .eigenvec files from Plink in R.
R SNP
updated 4.4 years ago by 102k • written 4.4 years ago by ▴ 70
13
votes
13
replies
797
views
Is reproducibility of identified variants in a gene important in Sanger sequencing?
reproducibility sanger sequencing variants
2.8 years ago by DanielC ▴ 150
13
votes
24
replies
2.8k
views
Error of bam-to-sam conversion using samtools
samtools TopHat2 RNA-Seq BAM SAM
updated 5.4 years ago by 119k • written 5.4 years ago by ▴ 480
13
votes
19
replies
3.7k
views
bbmerge not joining paired-end reads
bbmerge alignment
4.7 years ago by bioplanet ▴ 60
13
votes
16
replies
4.6k
views
6 follow
Confused about how to generate a consensus sequence after bwa
bwa samtools mpileup
3.6 years ago by DNAngel ▴ 210
13
votes
6
replies
8.8k
views
6 follow
MAF vs VAF
sequencing
4.4 years ago by lauren.wahyudi ▴ 40
13
votes
16
replies
4.5k
views
Mask or trim primer sequences in Amplicon sequencing
amplicon mask trimming fastq
5.6 years ago by Paul ★ 1.4k
13
votes
22
replies
8.1k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva combat batch effects
updated 4.9 years ago by 20 • written 5.1 years ago by ★ 1.2k
12
votes
28
replies
1.5k
views
Calculating the expression level of genes
Gene expression RNA-Seq R
4.2 years ago by Za ▴ 140
12
votes
11
replies
2.6k
views
How To Get Snp Genotypes
snp genotyping
updated 11.0 years ago by 11k • written 11.4 years ago by ▴ 20
12
votes
13
replies
2.0k
views
Gene Expression and Systems Biology (homework)
gene homework
7.1 years ago by sarathkurichiyil • 0
12
votes
8
replies
2.3k
views
How to change depth of sequence in RNA-seq fastq files
depth of sequence RNA-Seq
5.6 years ago by statfa ▴ 660
12
votes
10
replies
3.3k
views
Speed up BLASTp vs NCBI nr database
blast
6.2 years ago by biotech ▴ 560
12
votes
10
replies
2.0k
views
7 follow
SAM / BAM alignments
SAM BAM
5.6 years ago by John 13k
12
votes
12
replies
4.2k
views
Need A Script That Finds Whether A String In One Column Matches In Other Columns Of The Same Row
perl
updated 8.7 years ago by 94k • written 8.7 years ago by ★ 1.4k
12
votes
17
replies
3.5k
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
4.9 years ago by anonymous1192976466 ▴ 50
12
votes
14
replies
3.5k
views
bedtools intersect error?
ChIP-Seq bedtools intersect
3.5 years ago by star ▴ 290
1,000 results • Page 1 of 20
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Answer: How to read vcf file in python?
Comment: Gene-based and transcriptome-based profiling
Answer: Changing the x-axis in ggseqlogo in R
Answer: Installing ensembl-vep
Answer: Installing ensembl-vep
Answer: Changing the x-axis in ggseqlogo in R
Answer: Best way to detect CNV using WGS data
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Recent Replies
Answer: Problem in MarkDuplicates of picard by Pierre Lindenbaum 148k
VN in ` VN: ` should have a value. The htsjdk library _requires_ a value here: https://github.com/gkno/picard/blob/ffb68b5183efdaa561…
Comment: Gene-based and transcriptome-based profiling by Chris • 0
May I chat with you somewhere for more detail?
Answer: Is it possible to make certain branches of Snakemake conditional? by edsouza ▴ 30
Commenting to update: it seems that this issue is solved not at the level of the program, but at the level of the command line. `snakemake …
Comment: using gatk haplotypecaller for variants extraction by Nemo • 0
thanks @Ram, yes I searched for my question, and I read the link you sent. As I found I can use gatk haplotypecaller (I am skeptical yet) b…
Comment: How to deal with `'select()' returned 1:many mapping between keys and columns` w by LChart 640
> Is it because some genes do not have entrez ID? Yes. > If so, how should I deal with it? If you strictly require entrez IDs, then you…
Comment: using gatk haplotypecaller for variants extraction by Ram 36k
> I see the sample commands but I noticed they are for DNA seq data. So, it means I cannot use gatk haplotypecaller for rna seq data? You…
Comment: How to use RSEM to quantify genes and transcript expression from STAR outpute fi by Ram 36k
The "what is this supposed to be" part is the output prefix. Are you using `>&` when you mean to use `&>`? In any case, use `>rsem.out 2>rs…
Comment: Gene-based and transcriptome-based profiling by GenoMax 119k
It may be a case of semantics. When arrays were popular in early 2000s, people used the term "gene-based profiling". Both cases one is look…
Comment: Changing the x-axis in ggseqlogo in R by Ram 36k
I've moved the comment to an answer. Please accept it to mark the post as solved.
Comment: Changing the x-axis in ggseqlogo in R by margo ▴ 40
Thank you! That works!
Answer: Changing the x-axis in ggseqlogo in R by rpolicastro 9.4k
Untested but adding `+ scale_x_continuous(breaks=1:21, labels=-10:10)` to the returned ggplot2 object should work.
Answer: Installing ensembl-vep by tomas4482 ▴ 300
You can either create a new environment using Anaconda3 and download it via `conda install -n vep -c bioconda ensembl-vep` or install every…
Comment: Gene-based and transcriptome-based profiling by Chris • 0
Thank you so much for detailed answer! I am not confused about transcriptome-base profiling because I think it is RNA-Seq analysis. I only …
Answer: Concatenate information columns from multiple identical bed files. by Trivas ▴ 480
If you're comfortable using R, you can load the `.bed` files as tab delimited files, then `full_join` using `chr`, `start`, and `stop` as y…
Comment: Gene types to use for RNA counts case-control by i.sudbery 15k
Its not that we don't know which transcripts are poly-adenylated and which arn't - its just that that information is not encoded in the gen…
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