Profile Posts Awards
Show
all questions tools blogs news tutorials forum answers comments
Showing : questions
11
votes
6
replies
1.6k
views
How to merge set of bam files into one?
merge bam python pysam
updated 9 months ago by 44k • written 20 months ago by ▴ 180
0
votes
1
reply
588
views
how to download NCBI partially non-redundant nucleotide dataset for prokaryotes?
NCBI prokaryote
updated 18 months ago by 44k • written 2.4 years ago by ▴ 180
2
votes
2
replies
1.0k
views
How to relate a categorical external trait (case, control) into WGCNA network?
categorical eigen WGCNA gene relate
2.5 years ago by mrj ▴ 180
6
votes
3
replies
2.1k
views
How do I extract out ITS region from assembled whole genome sequence of a fungi?
genome Assembly alignment
updated 2.7 years ago by • 0 • written 5.4 years ago by ▴ 180
5
votes
4
replies
4.2k
views
why are all DiffBind tutorial's ATAC-seq peak intervals 400 bp for all intervals?
peak ATAC-seq intervals DiffBind consensus
updated 2.8 years ago by ★ 2.1k • written 2.9 years ago by ▴ 180
0
votes
0
replies
557
views
How to create motifs using biopython when the sequence object contain gaps (-)?
alphabet gaps motifs_create biopython
2.8 years ago by mrj ▴ 180
3
votes
3
replies
1.8k
views
How to identify the cell type computationally when you have a list of conserved cell type markers for mouse genome (as discovered by Seurat)?
Seurat scRNA-seq cell_type conserved_cell_type_markers
updated 2.9 years ago by ▴ 20 • written 2.9 years ago by ▴ 180
4
votes
2
replies
1.4k
views
In single cell RNA-seq, do we perform regular quality checks and adapter trimming before using cellranger?
cellranger adapter_trimming QC scRNA-seq
2.9 years ago by mrj ▴ 180
4
votes
3
replies
2.0k
views
How to import a BED file to ChIPseeker in order to visualize genome coverage plot?
ChIPseeker GRanges import ATAC-seq DiffBind
updated 2.9 years ago by ★ 3.0k • written 2.9 years ago by ▴ 180
2
votes
2
replies
977
views
How to check if a list of protein ID's are present in NCBI protein database?
esearch protein database NCBI
2.9 years ago by mrj ▴ 180
0
votes
0
replies
513
views
How to handle a esearch - elink empty result?
esearch ncbi protein elink
2.9 years ago by mrj ▴ 180
2
votes
2
replies
1.1k
views
How can I export raw count profile from DiffBind to be analyzed on DESeq2 separately?
raw DiffBind ATAC-seq profile export DESeq2 count
2.9 years ago by mrj ▴ 180
6
votes
5
replies
5.1k
views
How to parse cd-hit output (given in the description) to create a mapping file of clusters and representative sequence names?
clusters sequences mapping parse cd-hit
3.0 years ago by mrj ▴ 180
4
votes
2
replies
1.1k
views
What is a fast tool for searching sequence motifs in a large set of sequence files?
search fast sequence motif
3.0 years ago by mrj ▴ 180
1
vote
2
replies
2.4k
views
How to use MACS2 output for DESEQ2 differential analysis during ATAC-seq? How to get the intersect?
DESEQ2 ATAC-Seq intersect bedtools MACS2
3.0 years ago by mrj ▴ 180
2
votes
4
replies
1.1k
views
How to extract two genomic location numbers within the following fasta header?
fasta extract location genomic bash
3.0 years ago by mrj ▴ 180
4
votes
4
replies
1.1k
views
How to extract genomic upstream region of a protein identified by its NCBI accession number?
bedtools extract_upstream_region genomic_sequence NCBI
3.0 years ago by mrj ▴ 180
3
votes
4
replies
1.9k
views
How can I extract upstream regions in fasta for all blastx hits locally performed on nr database?
fasta nr blastx upstream region
3.0 years ago by mrj ▴ 180
2
votes
2
replies
1.3k
views
How to pipe awk of bed file into samtools to extract fasta sequences?
bedtools pipe samtools bash
updated 3.0 years ago by ▴ 450 • written 3.0 years ago by ▴ 180
5
votes
4
replies
2.4k
views
How do we process Kallisto output (continuous real values) for DESEQ2 analysis (which strictly require discrete count values)?
read-counts DESEQ2 differential-gene-expression kallisto
updated 5 months ago by 44k • written 3.1 years ago by ▴ 180
3
votes
2
replies
929
views
How to perform DESEQ2 analysis when there are three treatments (one of them being a reference)?
comparisons DESEQ2 expression multiple differential analysis
3.1 years ago by mrj ▴ 180
4
votes
2
replies
930
views
How to measure the similarity of operons from two species?
operon similarity bacteria
updated 3.3 years ago by ▴ 30 • written 4.4 years ago by ▴ 180
2
votes
2
replies
1.1k
views
How to map metatranscriptomics reads to a given genome (unannotated genome assembly)?
mapping genome alignment metatranscriptomics
3.3 years ago by mrj ▴ 180
2
votes
4
replies
1.2k
views
What are the disadvantages of increasing the sequencing depth of RNA-seq experiment?
NGS RNA-Seq sequencing depth transcriptome
3.5 years ago by mrj ▴ 180
2
votes
2
replies
1.9k
views
is quality evaluation of transcriptome assembly still required if my workflow is (good quality reads (fastp) -> bowtie2 alignment to reference genome…
RNA-seq transcriptome
updated 3.5 years ago by 145k • written 3.5 years ago by ▴ 180
1
vote
1
reply
880
views
Is genome coverage same as k-mer coverage for that genome?
genome coverage k-mer coverage
4.2 years ago by mrj ▴ 180
2
votes
2
replies
1.1k
views
reorder contigs into scaffold?
contig scaffold Assembly
updated 4.2 years ago by ▴ 240 • written 4.2 years ago by ▴ 180
0
votes
1
reply
910
views
How to interpret a contig statistics table?
Assembly WGS N50 contigs Soapdenovo2
4.2 years ago by mrj ▴ 180
1
vote
2
replies
889
views
How to detect different chromosomes from whole genome NGS reads of a fungi?
NGS scaffolds Assembly genome alignment
updated 4.6 years ago by ★ 3.8k • written 4.6 years ago by ▴ 180
4
votes
11
replies
1.8k
views
How to blastn a very short query sequence? Identifying telomeres in assembly
blastn blast shortquery telomere
updated 4.6 years ago by ▴ 20 • written 4.6 years ago by ▴ 180
5
votes
6
replies
1.4k
views
How to get a list of snp associated with any known cancer from NCBI with chromosomal locations?
SNP Cancer NCBI circos circularGenome
updated 4.7 years ago by ★ 1.2k • written 4.9 years ago by ▴ 180
0
votes
2
replies
2.0k
views
What are Metatranscriptomics databases?
metatranscriptomics metagenomics databases
updated 4.7 years ago by 3.7k • written 4.8 years ago by ▴ 180
32 results • Page 1 of 1
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6