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16
votes
5
replies
11k
views
Which genome fasta file and GTF file to be used in the RNA-Seq analysis
RNA-Seq gencode
updated 22 months ago by 45k • written 6.4 years ago by ▴ 340
1
vote
1
reply
3.6k
views
NS, AC, AN and AF in VCF file
VCF
updated 2.2 years ago by • 0 • written 3.3 years ago by ▴ 340
0
votes
1
reply
2.4k
views
Greengenes homepage
Greengenes
updated 4.5 years ago by 35k • written 4.5 years ago by ▴ 340
0
votes
1
reply
1.7k
views
Running Snakemake on the computing cluster
Snakemake HPC
updated 4.6 years ago by 45k • written 4.6 years ago by ▴ 340
0
votes
0
replies
2.0k
views
Comment: C: How does featurecounts deal with the output from Bowtie?
5.1 years ago by wangdp123 ▴ 340
0
votes
2
replies
2.0k
views
How does featurecounts deal with the output from Bowtie?
RNA-Seq Bowtie featureCounts
updated 5.1 years ago by 15k • written 5.1 years ago by ▴ 340
0
votes
1
reply
2.6k
views
Use PLINK2 to extract the specific variants
PLINK2
updated 5.2 years ago by 11k • written 5.3 years ago by ▴ 340
2
votes
1
reply
2.1k
views
The number of biological replicates and technical replicates in proteomics experiments
proteomics replicates
updated 5.5 years ago by 13k • written 5.5 years ago by ▴ 340
0
votes
0
replies
1.2k
views
Codon bias calculation tool
codon bias
5.5 years ago by wangdp123 ▴ 340
1
vote
1
reply
1.6k
views
GTF file in Ensembl database for RNA-Seq analysis
RNA-Seq GTF
updated 5.6 years ago by 20 • written 6.6 years ago by ▴ 340
0
votes
1
reply
1.0k
views
The codon table for all contigs/scaffolds/chromosomes of all genomes from Ensembl databases
Ensembl codon
updated 5.6 years ago by ★ 2.4k • written 5.6 years ago by ▴ 340
2
votes
1
reply
3.8k
views
Some questions regarding DESeq2
DESeq2 RNA-Seq
updated 5.6 years ago by ★ 7.8k • written 5.6 years ago by ▴ 340
6
votes
5
replies
1.5k
views
Forum: A free temporary HPC service for bioinformatic analysis
HPC
updated 2.4 years ago by 45k • written 5.7 years ago by ▴ 340
0
votes
0
replies
1.4k
views
Perform differential circular RNA expression
circRNA CIRCexplorer2
5.7 years ago by wangdp123 ▴ 340
1
vote
2
replies
4.2k
views
Paired-end metagenomics data for MEGAN analysis
MEGAN metagenomics
updated 5.7 years ago by ▴ 330 • written 6.0 years ago by ▴ 340
3
votes
9
replies
2.9k
views
The error generated by Rsamtools
Rsamtools Rsubread
updated 5.8 years ago by ★ 8.5k • written 5.8 years ago by ▴ 340
0
votes
0
replies
2.9k
views
Comment: C: The error generated by Rsamtools
updated 5.8 years ago by 45k • written 5.8 years ago by ▴ 340
0
votes
1
reply
2.9k
views
Comment: C: The error generated by Rsamtools
updated 5.8 years ago by 45k • written 5.8 years ago by ▴ 340
0
votes
1
reply
2.9k
views
Comment: C: The error generated by Rsamtools
5.8 years ago by wangdp123 ▴ 340
0
votes
1
reply
2.9k
views
Comment: C: The error generated by Rsamtools
5.8 years ago by wangdp123 ▴ 340
0
votes
1
reply
1.8k
views
The inclusion or exclusion of NR transcripts in RefSeq gene annotation in the RNA-Seq analysis
RNA-Seq RefSeq
updated 5.8 years ago by 20 • written 7.6 years ago by ▴ 340
3
votes
4
replies
1.7k
views
featurecounts output changes the underscores in the sample name into dots
featurecounts
updated 5.8 years ago by ★ 8.5k • written 5.8 years ago by ▴ 340
1
vote
2
replies
2.4k
views
Tool: GCevobase: an evolution-based database for GC content in eukaryotic genomes
GC-content genome evolution
updated 2.4 years ago by 45k • written 7.8 years ago by ▴ 340
3
votes
0
replies
2.6k
views
Tool: Tools and databases for gene co-linearity and conserved pairs and clusters in a large scale of genomes
gene-pair genome gene-order gene-synteny
updated 2.4 years ago by 45k • written 9.7 years ago by ▴ 340
1
vote
1
reply
1.7k
views
Deal with the time-course RNA-Seq datasets
RNA-Seq time-course
updated 6.3 years ago by 6.7k • written 6.3 years ago by ▴ 340
0
votes
1
reply
1.3k
views
The number of peaks in microRNA-Seq trimmed data
RNA-Seq microRNA
updated 6.3 years ago by ▴ 30 • written 6.3 years ago by ▴ 340
0
votes
1
reply
11k
views
Comment: C: Which genome fasta file and GTF file to be used in the RNA-Seq analysis
6.3 years ago by wangdp123 ▴ 340
2
votes
1
reply
1.8k
views
Is calcuNormFactors necessary in the calculation of RPKM?
RNA-Seq edgeR RPKM
updated 6.4 years ago by 90k • written 6.4 years ago by ▴ 340
0
votes
1
reply
4.1k
views
Comment: C: Primer sequences in fastq files from 16s rRNA experiment
6.6 years ago by wangdp123 ▴ 340
5
votes
6
replies
4.1k
views
Primer sequences in fastq files from 16s rRNA experiment
16s rRNA mothur
updated 6.6 years ago by ★ 2.2k • written 6.6 years ago by ▴ 340
0
votes
2
replies
1.9k
views
GATK best practice step-by-step command lines for Arabidopsis DNA-Seq data analysis
DNA-Seq Arabidopsis GATK
updated 6.6 years ago by 166k • written 6.6 years ago by ▴ 340
2
votes
1
reply
4.8k
views
How to calculate the mapping rate from BAM files generated from BWA
BWA
6.7 years ago by wangdp123 ▴ 340
0
votes
1
reply
4.3k
views
Comment: C: How to collect the phastCons and phyloP data from Ensembl
6.8 years ago by wangdp123 ▴ 340
0
votes
1
reply
4.3k
views
Comment: C: How to collect the phastCons and phyloP data from Ensembl
6.8 years ago by wangdp123 ▴ 340
10
votes
8
replies
4.3k
views
How to collect the phastCons and phyloP data from Ensembl
Ensembl phastCons phyloP
updated 6.8 years ago by 24k • written 6.8 years ago by ▴ 340
0
votes
1
reply
5.5k
views
STAR+Cufflinks for RNA-Seq analysis
RNA-Seq STAR Cufflinks
updated 6.8 years ago by 103k • written 6.8 years ago by ▴ 340
1
vote
4
replies
1.9k
views
How to link the assembly accession with the chromosome accession for prokaryotic representative genomes
NCBI prokaryotic genomes
7.0 years ago by wangdp123 ▴ 340
0
votes
1
reply
1.9k
views
Comment: A: How to link the assembly accession with the chromosome accession for prokaryotic
7.0 years ago by wangdp123 ▴ 340
0
votes
1
reply
4.9k
views
Smart-seq2 single-cell RNA-Seq
RNA-Seq Smart-seq2 single-cell
updated 7.0 years ago by ★ 4.2k • written 7.0 years ago by ▴ 340
0
votes
0
replies
3.9k
views
Comment: C: Can snakemake work with multiple nodes from HPC?
7.1 years ago by wangdp123 ▴ 340
3
votes
3
replies
5.9k
views
The difference between heatmap.2 and pheatmap
heatmap RNA-Seq
updated 7.1 years ago by 89k • written 7.1 years ago by ▴ 340
0
votes
1
reply
2.8k
views
Comment: C: Use OrthoDB to retrieve the orthologs between human and bacteria
7.1 years ago by wangdp123 ▴ 340
0
votes
1
reply
3.9k
views
Comment: C: Can snakemake work with multiple nodes from HPC?
7.1 years ago by wangdp123 ▴ 340
0
votes
1
reply
3.9k
views
Comment: C: Can snakemake work with multiple nodes from HPC?
7.1 years ago by wangdp123 ▴ 340
3
votes
6
replies
3.9k
views
Can snakemake work with multiple nodes from HPC?
snakemake HPC
7.1 years ago by wangdp123 ▴ 340
1
vote
4
replies
2.8k
views
Use OrthoDB to retrieve the orthologs between human and bacteria
orthologs orthoDB
updated 7.1 years ago by ▴ 740 • written 7.2 years ago by ▴ 340
0
votes
1
reply
2.7k
views
The m6A-Seq analysis
m6A-Seq ChIP-Seq
updated 7.1 years ago by ▴ 240 • written 7.4 years ago by ▴ 340
0
votes
1
reply
1.3k
views
q_value in cuffdiff results
RNA-Seq Cuffdiff
updated 7.1 years ago by 20 • written 7.2 years ago by ▴ 340
2
votes
1
reply
3.0k
views
The tools to plot the saturation curve for RNA-Seq
RNA-Seq
updated 7.2 years ago by ★ 3.2k • written 7.2 years ago by ▴ 340
0
votes
1
reply
3.5k
views
Comment: C: "Segmentation fault" error from running align function in Rsubread package
7.2 years ago by wangdp123 ▴ 340
89 results • Page 1 of 2
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