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16
votes
5
replies
8.3k
views
Which genome fasta file and GTF file to be used in the RNA-Seq analysis
RNA-Seq gencode
updated 4 months ago by 43k • written 4.8 years ago by ▴ 340
1
vote
1
reply
2.2k
views
NS, AC, AN and AF in VCF file
VCF
updated 7 months ago by • 0 • written 21 months ago by ▴ 340
0
votes
1
reply
1.7k
views
Greengenes homepage
Greengenes
updated 3.0 years ago by 35k • written 3.0 years ago by ▴ 340
0
votes
1
reply
1.3k
views
Running Snakemake on the computing cluster
Snakemake HPC
updated 3.0 years ago by 43k • written 3.1 years ago by ▴ 340
0
votes
2
replies
1.4k
views
How does featurecounts deal with the output from Bowtie?
RNA-Seq Bowtie featureCounts
updated 3.6 years ago by 14k • written 3.6 years ago by ▴ 340
0
votes
1
reply
2.0k
views
Use PLINK2 to extract the specific variants
PLINK2
updated 3.7 years ago by 10k • written 3.7 years ago by ▴ 340
2
votes
1
reply
1.5k
views
The number of biological replicates and technical replicates in proteomics experiments
proteomics replicates
updated 3.9 years ago by 13k • written 3.9 years ago by ▴ 340
0
votes
0
replies
969
views
Codon bias calculation tool
codon bias
4.0 years ago by wangdp123 ▴ 340
1
vote
1
reply
1.2k
views
GTF file in Ensembl database for RNA-Seq analysis
RNA-Seq GTF
updated 4.0 years ago by 20 • written 5.0 years ago by ▴ 340
0
votes
1
reply
648
views
The codon table for all contigs/scaffolds/chromosomes of all genomes from Ensembl databases
Ensembl codon
updated 4.0 years ago by ★ 2.4k • written 4.0 years ago by ▴ 340
2
votes
1
reply
2.2k
views
Some questions regarding DESeq2
DESeq2 RNA-Seq
updated 4.1 years ago by ★ 5.9k • written 4.1 years ago by ▴ 340
0
votes
0
replies
1.1k
views
Perform differential circular RNA expression
circRNA CIRCexplorer2
4.1 years ago by wangdp123 ▴ 340
1
vote
2
replies
3.1k
views
Paired-end metagenomics data for MEGAN analysis
MEGAN metagenomics
updated 4.2 years ago by ▴ 330 • written 4.4 years ago by ▴ 340
3
votes
9
replies
1.9k
views
The error generated by Rsamtools
Rsamtools Rsubread
updated 4.2 years ago by ★ 7.0k • written 4.2 years ago by ▴ 340
0
votes
1
reply
1.4k
views
The inclusion or exclusion of NR transcripts in RefSeq gene annotation in the RNA-Seq analysis
RNA-Seq RefSeq
updated 4.2 years ago by 20 • written 6.1 years ago by ▴ 340
3
votes
4
replies
1.2k
views
featurecounts output changes the underscores in the sample name into dots
featurecounts
updated 4.3 years ago by ★ 7.0k • written 4.3 years ago by ▴ 340
1
vote
1
reply
1.2k
views
Deal with the time-course RNA-Seq datasets
RNA-Seq time-course
updated 4.7 years ago by 6.5k • written 4.7 years ago by ▴ 340
0
votes
1
reply
904
views
The number of peaks in microRNA-Seq trimmed data
RNA-Seq microRNA
updated 4.8 years ago by ▴ 20 • written 4.8 years ago by ▴ 340
2
votes
1
reply
1.4k
views
Is calcuNormFactors necessary in the calculation of RPKM?
RNA-Seq edgeR RPKM
updated 4.8 years ago by 82k • written 4.8 years ago by ▴ 340
5
votes
6
replies
2.7k
views
Primer sequences in fastq files from 16s rRNA experiment
16s rRNA mothur
updated 5.0 years ago by ★ 2.2k • written 5.0 years ago by ▴ 340
0
votes
2
replies
1.5k
views
GATK best practice step-by-step command lines for Arabidopsis DNA-Seq data analysis
DNA-Seq Arabidopsis GATK
updated 5.1 years ago by 161k • written 5.1 years ago by ▴ 340
2
votes
1
reply
4.1k
views
How to calculate the mapping rate from BAM files generated from BWA
BWA
5.1 years ago by wangdp123 ▴ 340
8
votes
8
replies
2.7k
views
How to collect the phastCons and phyloP data from Ensembl
Ensembl phastCons phyloP
updated 5.2 years ago by 23k • written 5.2 years ago by ▴ 340
0
votes
1
reply
4.8k
views
STAR+Cufflinks for RNA-Seq analysis
RNA-Seq STAR Cufflinks
updated 5.2 years ago by 100k • written 5.2 years ago by ▴ 340
1
vote
4
replies
1.3k
views
How to link the assembly accession with the chromosome accession for prokaryotic representative genomes
NCBI prokaryotic genomes
5.4 years ago by wangdp123 ▴ 340
0
votes
1
reply
4.4k
views
Smart-seq2 single-cell RNA-Seq
RNA-Seq Smart-seq2 single-cell
updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by ▴ 340
3
votes
3
replies
4.4k
views
The difference between heatmap.2 and pheatmap
heatmap RNA-Seq
updated 5.5 years ago by 87k • written 5.5 years ago by ▴ 340
3
votes
6
replies
2.9k
views
Can snakemake work with multiple nodes from HPC?
snakemake HPC
5.5 years ago by wangdp123 ▴ 340
1
vote
4
replies
2.0k
views
Use OrthoDB to retrieve the orthologs between human and bacteria
orthologs orthoDB
updated 5.5 years ago by ▴ 740 • written 5.6 years ago by ▴ 340
0
votes
1
reply
2.2k
views
The m6A-Seq analysis
m6A-Seq ChIP-Seq
updated 5.6 years ago by ▴ 240 • written 5.9 years ago by ▴ 340
0
votes
1
reply
1.0k
views
q_value in cuffdiff results
RNA-Seq Cuffdiff
updated 5.6 years ago by 20 • written 5.6 years ago by ▴ 340
2
votes
1
reply
2.4k
views
The tools to plot the saturation curve for RNA-Seq
RNA-Seq
updated 5.6 years ago by ★ 3.1k • written 5.6 years ago by ▴ 340
1
vote
5
replies
2.5k
views
"Segmentation fault" error from running align function in Rsubread package
RNA-Seq Rsubread
updated 5.7 years ago by 19k • written 5.7 years ago by ▴ 340
0
votes
5
replies
2.4k
views
The failed compilation of Rsubread
Rsubread RNA-Seq
5.8 years ago by wangdp123 ▴ 340
6
votes
3
replies
7.4k
views
What is the difference between single-cell RNA-Seq and typical RNA-Seq in terms of data analysis procedure
single-cell RNA-Seq
updated 5.9 years ago by 104k • written 5.9 years ago by ▴ 340
4
votes
2
replies
1.5k
views
samtools and I/O redirection
samtools
5.9 years ago by wangdp123 ▴ 340
0
votes
4
replies
3.2k
views
The errors reported when running snakemake file with log function
snakemake
updated 5.9 years ago by 104k • written 5.9 years ago by ▴ 340
2
votes
1
reply
4.1k
views
The logging file for snakemake
snakemake log
5.9 years ago by wangdp123 ▴ 340
0
votes
1
reply
2.5k
views
How to normalize the bam files for RNA-Seq samples for visualization
RNA-Seq normalization visualize
updated 6.0 years ago by ★ 1.9k • written 6.0 years ago by ▴ 340
0
votes
0
replies
924
views
The estimate index of codon bias
codon bias
6.1 years ago by wangdp123 ▴ 340
0
votes
1
reply
1.0k
views
Cluster genes based on their codon usage
codon usage cluster gene
6.1 years ago by wangdp123 ▴ 340
0
votes
1
reply
1.1k
views
Process the VCF files for a huge number of samples
VCF SNP InDel Exome-Seq
6.2 years ago by wangdp123 ▴ 340
9
votes
3
replies
14k
views
How to find the hub genes in the gene co-expression network constructed by WGCNA
WGCNA hub gene
updated 6.3 years ago by 87k • written 6.3 years ago by ▴ 340
39
votes
25
replies
23k
views
8 follow
The RNA-Seq data input for WGCNA in terms of gene co-expression network construction
WGCNA network
updated 6.5 years ago by 87k • written 6.5 years ago by ▴ 340
0
votes
0
replies
1.1k
views
The strategy to annotate the transcriptional factors from transcripts
TF annotation
6.6 years ago by wangdp123 ▴ 340
3
votes
3
replies
2.5k
views
Draw the phylogeny from RNA-Seq data
RNA-Seq phylogeny species tissues treatment
updated 6.7 years ago by 20 • written 6.8 years ago by ▴ 340
1
vote
2
replies
1.2k
views
How to understand "between_species_paralog" in Ensembl and EnsemblGenomes
Ensembl paralogs EnsemblGenomes
updated 6.8 years ago by 23k • written 6.8 years ago by ▴ 340
1
vote
1
reply
4.8k
views
How to rank genes prepared for GSEA analysis with TopGO
TopGO GSEA RNA-Seq
updated 6.8 years ago by ★ 1.7k • written 6.8 years ago by ▴ 340
0
votes
1
reply
1.9k
views
How to obtain more GO terms for transcripts
Gene ontology de novo assembly
updated 6.9 years ago by ▴ 960 • written 6.9 years ago by ▴ 340
4
votes
11
replies
3.9k
views
Software for GO enrichment based on own DEGs and GO annotation.
GO enrichment
updated 6.9 years ago by ★ 1.4k • written 6.9 years ago by ▴ 340
57 results • Page 1 of 2
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