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1
vote
5
replies
1.3k
views
How can I analyze this data in Deseq?
deseq rnaseq deseq2 R
5.6 years ago by MAPK ★ 2.1k
5
votes
7
replies
2.0k
views
Extract coverage from each nucleotide position of a genome in a bam file
bam bed coverage
5.6 years ago by MAPK ★ 2.1k
9
votes
4
replies
6.4k
views
coverage plot for all chromosomes
RNA-Seq
5.6 years ago by MAPK ★ 2.1k
7
votes
5
replies
24k
views
How to perform KEGG pathway analysis in R?
KEGG
updated 5.8 years ago by ▴ 20 • written 7.1 years ago by ★ 2.1k
0
votes
1
reply
860
views
Where can I find Intergenic regions (non-rRNA), retrotransposons and Ribosomal RNA sequences?
next-gen assembly
updated 5.9 years ago by 35k • written 5.9 years ago by ★ 2.1k
3
votes
4
replies
1.1k
views
How can I map certain values for gene locus against genome?
r
5.9 years ago by MAPK ★ 2.1k
5
votes
11
replies
1.4k
views
Adaptor trimming for RNAseq
RNA-Seq
5.9 years ago by MAPK ★ 2.1k
0
votes
2
replies
1.1k
views
Tools to predict microRNAs in Ascomycota(Fungus)
smallRNA RNA-Seq microRNA
updated 6.0 years ago by ★ 2.4k • written 6.0 years ago by ★ 2.1k
11
votes
6
replies
3.0k
views
How do I loop over a list of gene symbols to extract sequences from NCBI?
ncbi eutils bash
6.0 years ago by MAPK ★ 2.1k
18
votes
7
replies
4.3k
views
How do I set filter for NCBI esearch to get fasta for Genes only?
esearch
6.0 years ago by MAPK ★ 2.1k
9
votes
3
replies
1.9k
views
DEseq2 logfold interpretation
DEseq2 RNA-Seq
6.0 years ago by MAPK ★ 2.1k
6
votes
5
replies
1.5k
views
Extract sequence ID from Fasta for a given sequence
Fasta
updated 6.0 years ago by ★ 3.8k • written 6.0 years ago by ★ 2.1k
0
votes
3
replies
2.2k
views
How to submit paired-end fastq files of a single sample to SRA?
sra
updated 6.0 years ago by 20 • written 6.2 years ago by ★ 2.1k
0
votes
0
replies
1.8k
views
Microbiome data analysis using Vegan R tool
vegan microbiome
updated 6.0 years ago by 20 • written 6.1 years ago by ★ 2.1k
1
vote
3
replies
1.3k
views
What is the fate of low coverage region during Trinity assembly of transcriptome data?
Trinity transcriptome Assembly
6.0 years ago by MAPK ★ 2.1k
0
votes
2
replies
1.4k
views
Dealing with NAs in microbiome transcriptome count data for differential expression
RNA-Seq Deseq2 microbiome
6.0 years ago by MAPK ★ 2.1k
3
votes
10
replies
2.7k
views
How do you identify the contigs from trinity assembly?
Trinity Assembly blast
6.1 years ago by MAPK ★ 2.1k
5
votes
4
replies
2.3k
views
R programming: match and rearrange
R
updated 6.1 years ago by 44k • written 9.5 years ago by ★ 2.1k
3
votes
13
replies
6.6k
views
How can I submit paired-end SRA data to NCBI?
sra ncbi
updated 6.1 years ago by 20 • written 6.1 years ago by ★ 2.1k
27
votes
7
replies
7.0k
views
Why do R1 and R2 compressed files have different size
fastq gzip
updated 6.1 years ago by 14k • written 6.1 years ago by ★ 2.1k
0
votes
0
replies
1.0k
views
Contig assembly in different genomes of the same species
Assembly
6.1 years ago by MAPK ★ 2.1k
5
votes
11
replies
2.9k
views
Help with multi-factor Deseq analysis
deseq2 rna-seq
6.1 years ago by MAPK ★ 2.1k
8
votes
4
replies
1.1k
views
Retrieve gene length and cds locus informartion
ncbi batch_entrez
updated 6.2 years ago by 146k • written 6.2 years ago by ★ 2.1k
0
votes
1
reply
1.1k
views
Tools to construct gene model
gene model intron exon domain
updated 6.2 years ago by 88k • written 6.2 years ago by ★ 2.1k
10
votes
8
replies
7.4k
views
What are the major differences between plink and plink2?
plink
updated 6.2 years ago by 11k • written 6.6 years ago by ★ 2.1k
3
votes
2
replies
1.4k
views
How to obtain alignment figure?
clustalw alignment
updated 6.2 years ago by 21k • written 6.2 years ago by ★ 2.1k
5
votes
10
replies
4.4k
views
Get multiple snps coverage (allelic depth) from bam files
bam sequencing genotype
updated 2.2 years ago by 44k • written 8.9 years ago by ★ 2.1k
6
votes
1
reply
7.6k
views
How do you convert single end sam file to fastq?
samtfastq sam fastq
updated 6.2 years ago by 164k • written 6.2 years ago by ★ 2.1k
9
votes
5
replies
4.4k
views
When do you strictly need to know the adapter sequence to trim NGS data?
adapter NGS trimming
updated 6.2 years ago by 5.8k • written 6.2 years ago by ★ 2.1k
4
votes
10
replies
1.6k
views
How do you get rid of reads with matching pattern in fastq
fastq
updated 6.2 years ago by 146k • written 6.2 years ago by ★ 2.1k
8
votes
4
replies
2.2k
views
Command to count reads in fastq file with last bases
fastq readcount
updated 6.2 years ago by ★ 2.1k • written 6.2 years ago by ★ 2.1k
6
votes
4
replies
2.2k
views
How do I completely get rid of adapter sequence
smallRNAseq trimming adapter
6.2 years ago by MAPK ★ 2.1k
8
votes
7
replies
6.8k
views
Separate unaligned reads in fastq format using bowtie
bowtie fastq
6.2 years ago by MAPK ★ 2.1k
5
votes
6
replies
1.8k
views
Small RNAseq data with untrimmed reads left after trimming process
RNA-Seq smallRNAseq trimming adapters
updated 6.2 years ago by 35k • written 6.2 years ago by ★ 2.1k
2
votes
6
replies
2.9k
views
How do you decide the minimum length for the adapter that needs trimming for small RNAseq
trimmomatic trimming adapter smallRNAseq
6.2 years ago by MAPK ★ 2.1k
4
votes
2
replies
2.6k
views
Rstudio like IDE for perl
perl
updated 6.2 years ago by ▴ 380 • written 6.2 years ago by ★ 2.1k
8
votes
7
replies
3.0k
views
How to format nr database for blastp?
blastp makeblastdb
updated 6.2 years ago by 35k • written 6.2 years ago by ★ 2.1k
7
votes
3
replies
3.7k
views
How to determine which adapter to use while trimming?
trimmomatic NGS fastq adapter
updated 6.3 years ago by ▴ 120 • written 6.3 years ago by ★ 2.1k
4
votes
3
replies
2.5k
views
Long read alignment for MEGAN6
Megan alignment Long-read alignment
updated 6.3 years ago by ▴ 250 • written 6.3 years ago by ★ 2.1k
4
votes
2
replies
3.6k
views
pfam_scan.pl can't find the pfamdb
pfamdb
updated 2.9 years ago by • 0 • written 6.3 years ago by ★ 2.1k
3
votes
3
replies
1.9k
views
How can I create LASTdb for nr.gz data?
last alignement
updated 6.3 years ago by 35k • written 6.3 years ago by ★ 2.1k
0
votes
0
replies
2.0k
views
Megan microbiome analysis
megan
6.3 years ago by MAPK ★ 2.1k
0
votes
1
reply
1.9k
views
ContEst sample contamination error
Contest
updated 6.3 years ago by 164k • written 8.4 years ago by ★ 2.1k
5
votes
3
replies
5.7k
views
RAxML multi-threading option in HPC cluster
raxml phylogenetics
6.3 years ago by MAPK ★ 2.1k
3
votes
1
reply
6.1k
views
How to tell the best model for ML analysis using RaxML?
Raxml modeltest phylogenetics
updated 6.3 years ago by 55k • written 6.3 years ago by ★ 2.1k
0
votes
2
replies
1.8k
views
PBS script not able to locate the tool
pbs
6.4 years ago by MAPK ★ 2.1k
1
vote
5
replies
5.3k
views
RAXML phylogenetics analysis
RAXML
6.4 years ago by MAPK ★ 2.1k
0
votes
2
replies
2.6k
views
How to run microsynteny plotter from McScan?
Mcscan microsynteny
updated 2.1 years ago by ▴ 20 • written 6.6 years ago by ★ 2.1k
52
votes
15
replies
58k
views
11 follow
How to extract specific chromosome from vcf file
vcf
updated 2.0 years ago by ▴ 600 • written 8.3 years ago by ★ 2.1k
0
votes
1
reply
1.7k
views
How to run microsynteny using MCscan?
mcscan
updated 6.6 years ago by 20 • written 6.6 years ago by ★ 2.1k
238 results • Page 2 of 5
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