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questions
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
5.7 years ago by
MAPK
★ 2.1k
9
votes
4
replies
6.4k
views
coverage plot for all chromosomes
RNA-Seq
5.7 years ago by
MAPK
★ 2.1k
7
votes
5
replies
24k
views
How to perform KEGG pathway analysis in R?
KEGG
updated 5.9 years ago by
Stiofan
▴ 20 • written 7.1 years ago by
MAPK
★ 2.1k
0
votes
1
reply
867
views
Where can I find Intergenic regions (non-rRNA), retrotransposons and Ribosomal RNA sequences?
next-gen
assembly
updated 6.0 years ago by
h.mon
35k • written 6.0 years ago by
MAPK
★ 2.1k
3
votes
4
replies
1.2k
views
How can I map certain values for gene locus against genome?
r
6.0 years ago by
MAPK
★ 2.1k
5
votes
11
replies
1.4k
views
Adaptor trimming for RNAseq
RNA-Seq
6.0 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
Buffo
★ 2.4k • written 6.0 years ago by
MAPK
★ 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
4.4k
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
michael.ante
★ 3.9k • written 6.0 years ago by
MAPK
★ 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
Biostar
20 • written 6.2 years ago by
MAPK
★ 2.1k
0
votes
0
replies
1.8k
views
Microbiome data analysis using Vegan R tool
vegan
microbiome
updated 6.1 years ago by
Biostar
20 • written 6.2 years ago by
MAPK
★ 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
6.1 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
6.1 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
Ram
44k • written 9.5 years ago by
MAPK
★ 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
Biostar
20 • written 6.2 years ago by
MAPK
★ 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
dariober
15k • written 6.1 years ago by
MAPK
★ 2.1k
0
votes
0
replies
1.0k
views
Contig assembly in different genomes of the same species
Assembly
6.2 years ago by
MAPK
★ 2.1k
5
votes
11
replies
2.9k
views
Help with multi-factor Deseq analysis
deseq2
rna-seq
6.2 years ago by
MAPK
★ 2.1k
8
votes
4
replies
1.2k
views
Retrieve gene length and cds locus informartion
ncbi
batch_entrez
updated 6.2 years ago by
GenoMax
146k • written 6.2 years ago by
MAPK
★ 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
Kevin Blighe
88k • written 6.2 years ago by
MAPK
★ 2.1k
10
votes
8
replies
7.5k
views
What are the major differences between plink and plink2?
plink
updated 6.2 years ago by
chrchang523
11k • written 6.7 years ago by
MAPK
★ 2.1k
3
votes
2
replies
1.5k
views
How to obtain alignment figure?
clustalw
alignment
updated 6.2 years ago by
Joe
21k • written 6.2 years ago by
MAPK
★ 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
Ram
44k • written 9.0 years ago by
MAPK
★ 2.1k
6
votes
1
reply
7.7k
views
How do you convert single end sam file to fastq?
samtfastq
sam
fastq
updated 6.3 years ago by
Pierre Lindenbaum
164k • written 6.3 years ago by
MAPK
★ 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 6.3 years ago by
Gjain
5.8k • written 6.3 years ago by
MAPK
★ 2.1k
4
votes
10
replies
1.6k
views
How do you get rid of reads with matching pattern in fastq
fastq
updated 6.3 years ago by
GenoMax
146k • written 6.3 years ago by
MAPK
★ 2.1k
8
votes
4
replies
2.2k
views
Command to count reads in fastq file with last bases
fastq
readcount
updated 6.3 years ago by
Eric Lim
★ 2.2k • written 6.3 years ago by
MAPK
★ 2.1k
6
votes
4
replies
2.2k
views
How do I completely get rid of adapter sequence
smallRNAseq
trimming
adapter
6.3 years ago by
MAPK
★ 2.1k
8
votes
7
replies
6.8k
views
Separate unaligned reads in fastq format using bowtie
bowtie
fastq
6.3 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 6.3 years ago by
h.mon
35k • written 6.3 years ago by
MAPK
★ 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
6.3 years ago by
MAPK
★ 2.1k
4
votes
2
replies
2.7k
views
Rstudio like IDE for perl
perl
updated 6.3 years ago by
Dattatray Mongad
▴ 380 • written 6.3 years ago by
MAPK
★ 2.1k
8
votes
7
replies
3.0k
views
How to format nr database for blastp?
blastp
makeblastdb
updated 6.3 years ago by
h.mon
35k • written 6.3 years ago by
MAPK
★ 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
sschmeier
▴ 120 • written 6.3 years ago by
MAPK
★ 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
buchfink
▴ 250 • written 6.3 years ago by
MAPK
★ 2.1k
4
votes
2
replies
3.6k
views
pfam_scan.pl can't find the pfamdb
pfamdb
updated 2.9 years ago by
Wahbi
• 0 • written 6.3 years ago by
MAPK
★ 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
h.mon
35k • written 6.3 years ago by
MAPK
★ 2.1k
0
votes
0
replies
2.0k
views
Megan microbiome analysis
megan
6.4 years ago by
MAPK
★ 2.1k
0
votes
1
reply
1.9k
views
ContEst sample contamination error
Contest
updated 6.4 years ago by
Pierre Lindenbaum
164k • written 8.4 years ago by
MAPK
★ 2.1k
5
votes
3
replies
5.8k
views
RAxML multi-threading option in HPC cluster
raxml
phylogenetics
6.4 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 6.4 years ago by
Michael
55k • written 6.4 years ago by
MAPK
★ 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
Nelo
▴ 20 • written 6.6 years ago by
MAPK
★ 2.1k
52
votes
15
replies
59k
views
11 follow
How to extract specific chromosome from vcf file
vcf
updated 2.1 years ago by
beausoleilmo
▴ 600 • written 8.3 years ago by
MAPK
★ 2.1k
0
votes
1
reply
1.7k
views
How to run microsynteny using MCscan?
mcscan
updated 6.6 years ago by
Biostar
20 • written 6.6 years ago by
MAPK
★ 2.1k
238 results • Page
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