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41
votes
55
replies
9.6k
views
6 follow
hash function for DNA sequences
hash hashing DNA
6.8 years ago by midox ▴ 290
27
votes
17
replies
16k
views
12 follow
Dotplot for filtered pathways result
pathways ggplot2 clusterProfiler r dotplot
14 months ago by Leite ★ 1.2k
24
votes
25
replies
5.4k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq beta diversity metagenomics
2.5 years ago by dpc ▴ 240
23
votes
22
replies
36k
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 9 weeks ago by • 0 • written 4.7 years ago by ▴ 250
23
votes
10
replies
4.9k
views
How to predict individual ethnicity information by using hapmap data
SNP Ethnicity Hapmap
updated 21 months ago by 84k • written 4.9 years ago by ▴ 40
22
votes
19
replies
2.4k
views
targets of a list of miRNAs
miRNAs RNA-Seq DEanalysis target-prediction
6.3 years ago by fi1d18 ★ 4.1k
22
votes
20
replies
2.0k
views
what is the prefered strategy to treat with blast-less transcriptomes from RNA-seq
RNA-Seq blast gene genome Forum
6.6 years ago by Farbod ★ 3.3k
19
votes
15
replies
25k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink SNP
updated 6 months ago by 37k • written 7.1 years ago by ▴ 180
19
votes
43
replies
3.9k
views
Annotation of huge number of CNV files
CNV annotation TCGA
4.5 years ago by nazaninhoseinkhan ▴ 490
18
votes
19
replies
1.5k
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 9 weeks ago by 37k • written 4.1 years ago by • 0
18
votes
7
replies
745
views
How to calculate if statistically a variable of a bulk RNA-seq affects the comparison of interest?
DESeq2 Variable RNA-seq
4 months ago by Rafael Soler ★ 1.1k
18
votes
4
replies
8.0k
views
How To Find Rna-Seq Data Of Published Papers?
bioinformatics next-gen rna-seq geo
9.5 years ago by user ▴ 930
17
votes
19
replies
2.0k
views
Sorting sequences according header
software error sequence Assembly next-gen
6.4 years ago by Gian77 ▴ 60
17
votes
37
replies
3.2k
views
No alias or index file found for protein database
next-gen software error sequence
updated 3.7 years ago by 20 • written 3.8 years ago by ▴ 470
17
votes
13
replies
5.3k
views
7 follow
BWA: Why paired reads mapped to different chromosome?
alignment genome sequencing
5.7 years ago by lghust2011 ▴ 100
17
votes
8
replies
1.8k
views
Number of unique authors in PubMed in last 10 years
PubMed
6.9 years ago by nejc ▴ 50
16
votes
14
replies
13k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters trimmomatic RNA-seq
4.6 years ago by salamandra ▴ 510
16
votes
8
replies
1.6k
views
8 follow
What are the most important unresolved problems in Bioinformatics?
problem unresolved bioinformatics
updated 6.3 years ago by 20 • written 6.3 years ago by ★ 2.4k
16
votes
10
replies
4.6k
views
6 follow
Powerful desktop computer for genomics
next-gen sequencing ChIP-Seq RNA-Seq
6.7 years ago by Alternative ▴ 270
16
votes
21
replies
1.5k
views
Why there are different hit for a same gene in different species
gene blast ortholog paralog
6.3 years ago by Farbod ★ 3.3k
16
votes
38
replies
15k
views
Differential gene Analysis by Limma
Limma Microarray R
updated 9 months ago by 37k • written 8.0 years ago by ▴ 920
16
votes
16
replies
2.3k
views
Using DESeq2 results for building a classifier
deseq2 RNA-Seq differentially expressed genes
4.9 years ago by bioinfo456 ▴ 150
16
votes
18
replies
3.5k
views
8 follow
Python Program to read .fasta file to .txt file
Python
updated 3.4 years ago by ★ 22k • written 3.4 years ago by • 0
16
votes
17
replies
2.6k
views
6 follow
RNA seq pipeline
RNA-Seq
5.3 years ago by dimitrischat ▴ 180
15
votes
14
replies
2.2k
views
Penalty model of BWA MEM and BOWTIE2?
RNA-Seq bwa mem bowtie2 alignment
5.1 years ago by John ▴ 260
15
votes
14
replies
1.3k
views
how can interpret these biologically weird results?
RNA-Seq
updated 2.0 years ago by 20 • written 5.2 years ago by ▴ 330
15
votes
19
replies
1.3k
views
trimmomaric command for a fasta file?
trimmomatic
updated 4.8 years ago by 37k • written 4.8 years ago by • 0
14
votes
17
replies
4.8k
views
HiSeq 4000 PhiX screening and removal using bbduk
spikein filtering bbmap bbduk phix
5.5 years ago by Anand Rao ▴ 550
14
votes
8
replies
4.5k
views
Unable To Replicate Splice Junction In Tophat
tophat2 bam
9.3 years ago by Dan D 7.4k
14
votes
30
replies
2.4k
views
Download GTF/GFF annotation data for NT database, not by organism (for STAR alignment)
RNA-Seq rna-seq alignment next-gen
3.7 years ago by Malka ▴ 70
14
votes
18
replies
4.0k
views
GATK Haplotype Caller
next-gen GATK haplotype caller contigs
updated 6.1 years ago by 20 • written 6.3 years ago by ▴ 50
14
votes
5
replies
2.6k
views
bioinformatics basic training
genome Tutorial
updated 11 months ago by 37k • written 8.2 years ago by • 0
14
votes
16
replies
1.2k
views
Why are some mapped reads not mapped completely?
RNA-Seq mapping
updated 2.2 years ago by 14k • written 2.2 years ago by ▴ 80
13
votes
7
replies
5.7k
views
Why some probes have "NA" for gene symbol and Entrez ID?
affymetrix microarray NA genesymbol
updated 6.2 years ago by 20 • written 6.2 years ago by ▴ 230
13
votes
6
replies
9.6k
views
6 follow
MAF vs VAF
sequencing
4.9 years ago by lauren.wahyudi ▴ 40
13
votes
22
replies
8.7k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva combat batch effects
updated 5.4 years ago by 20 • written 5.6 years ago by ★ 1.3k
13
votes
13
replies
923
views
Is reproducibility of identified variants in a gene important in Sanger sequencing?
reproducibility sanger sequencing variants
3.3 years ago by DanielC ▴ 160
13
votes
16
replies
4.8k
views
Mask or trim primer sequences in Amplicon sequencing
amplicon mask trimming fastq
6.1 years ago by Paul ★ 1.5k
13
votes
24
replies
3.2k
views
Error of bam-to-sam conversion using samtools
samtools TopHat2 RNA-Seq BAM SAM
updated 5.9 years ago by 125k • written 5.9 years ago by ▴ 480
13
votes
16
replies
5.2k
views
6 follow
Confused about how to generate a consensus sequence after bwa
bwa samtools mpileup
4.1 years ago by DNAngel ▴ 240
13
votes
19
replies
4.1k
views
bbmerge not joining paired-end reads
bbmerge alignment
5.2 years ago by bioplanet ▴ 60
13
votes
13
replies
7.7k
views
How to do pca plot from .eigenval and .eigenvec files from Plink in R.
R SNP
updated 4.9 years ago by 102k • written 4.9 years ago by ▴ 70
12
votes
28
replies
1.8k
views
Calculating the expression level of genes
Gene expression RNA-Seq R
4.7 years ago by Za ▴ 140
12
votes
11
replies
2.7k
views
How To Get Snp Genotypes
snp genotyping
updated 11.4 years ago by 11k • written 11.8 years ago by ▴ 20
12
votes
8
replies
546
views
Align 16S sequence to a reference
16S sequence alignment
updated 4 months ago by 2.9k • written 4 months ago by ▴ 120
12
votes
10
replies
2.2k
views
7 follow
SAM / BAM alignments
SAM BAM
6.1 years ago by John 13k
12
votes
8
replies
2.5k
views
How to change depth of sequence in RNA-seq fastq files
depth of sequence RNA-Seq
6.0 years ago by statfa ▴ 680
12
votes
14
replies
4.1k
views
bedtools intersect error?
ChIP-Seq bedtools intersect
4.0 years ago by star ▴ 330
12
votes
10
replies
3.5k
views
Speed up BLASTp vs NCBI nr database
blast
6.7 years ago by biotech ▴ 560
12
votes
17
replies
3.8k
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
5.3 years ago by anonymous1192976466 ▴ 50
1,000 results • Page 1 of 20
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Comment: DESeq2 results function runs very slow on Windows 10 by i.sudbery 16k
This would also explain the performance difference - the code is running on multiple cores on the Apple, but only a single core on Windows.
Comment: RNA Editing data from RNA-seq by i.sudbery 16k
You usually need DNA sequencing data as well as RNAseq data to identify RNA editing events.
Comment: How to find the most frequent alternative-splicing event from DEXSEQ data? by i.sudbery 16k
What do you mean be "most frequent alternative splicing event"? Do you mean which type of change (cassette exon, alternative 5' splice-site…
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I don't see genes in this location on the standard sheep genome either. The image you've included above doesn't show the gene annotation. B…
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I found the answer and I share it with you. setwd("directory/of/Treemix/results") source("plotting_funcs.R") get_f("…
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This isn't a matter of "know[ing] the inner workings of PLINK2". It's about clear communication and debugging practice. You never posted …
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No idea about the first error. I rarely used GATK, but I have a guess regarding the second error. 1) emit-ref-confidence = ERC, 2) the soft…
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I feel like I reproduced all the information I could, as I do not know the inner workings of PLINK2 and this is all I know of the problem. …
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Have you looked at any tutorials? Three are many out there. ([1][1], [2][2], [3][3], [etc.][4]) Do you have a preferred language? [1]: …
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