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11
votes
6
replies
1.3k
views
How to merge set of bam files into one?
merge bam python pysam
updated 4 months ago by 43k • written 15 months ago by ▴ 170
0
votes
1
reply
482
views
how to download NCBI partially non-redundant nucleotide dataset for prokaryotes?
NCBI prokaryote
updated 13 months ago by 43k • written 23 months ago by ▴ 170
2
votes
2
replies
854
views
How to relate a categorical external trait (case, control) into WGCNA network?
categorical eigen WGCNA gene relate
2.1 years ago by mrj ▴ 170
5
votes
3
replies
1.9k
views
How do I extract out ITS region from assembled whole genome sequence of a fungi?
genome Assembly alignment
updated 2.3 years ago by • 0 • written 5.0 years ago by ▴ 170
5
votes
4
replies
3.7k
views
why are all DiffBind tutorial's ATAC-seq peak intervals 400 bp for all intervals?
peak ATAC-seq intervals DiffBind consensus
updated 2.4 years ago by ★ 2.0k • written 2.5 years ago by ▴ 170
0
votes
0
replies
507
views
How to create motifs using biopython when the sequence object contain gaps (-)?
alphabet gaps motifs_create biopython
2.4 years ago by mrj ▴ 170
3
votes
3
replies
1.7k
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 2.5 years ago by ▴ 20 • written 2.5 years ago by ▴ 170
4
votes
2
replies
1.3k
views
In single cell RNA-seq, do we perform regular quality checks and adapter trimming before using cellranger?
cellranger adapter_trimming QC scRNA-seq
2.5 years ago by mrj ▴ 170
4
votes
3
replies
1.8k
views
How to import a BED file to ChIPseeker in order to visualize genome coverage plot?
ChIPseeker GRanges import ATAC-seq DiffBind
updated 2.5 years ago by ★ 2.9k • written 2.5 years ago by ▴ 170
2
votes
2
replies
881
views
How to check if a list of protein ID's are present in NCBI protein database?
esearch protein database NCBI
2.5 years ago by mrj ▴ 170
0
votes
0
replies
456
views
How to handle a esearch - elink empty result?
esearch ncbi protein elink
2.5 years ago by mrj ▴ 170
2
votes
2
replies
1.0k
views
How can I export raw count profile from DiffBind to be analyzed on DESeq2 separately?
raw DiffBind ATAC-seq profile export DESeq2 count
2.5 years ago by mrj ▴ 170
6
votes
5
replies
4.7k
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
2.6 years ago by mrj ▴ 170
4
votes
2
replies
1.0k
views
What is a fast tool for searching sequence motifs in a large set of sequence files?
search fast sequence motif
2.6 years ago by mrj ▴ 170
1
vote
2
replies
2.1k
views
How to use MACS2 output for DESEQ2 differential analysis during ATAC-seq? How to get the intersect?
DESEQ2 ATAC-Seq intersect bedtools MACS2
2.6 years ago by mrj ▴ 170
2
votes
4
replies
982
views
How to extract two genomic location numbers within the following fasta header?
fasta extract location genomic bash
2.6 years ago by mrj ▴ 170
4
votes
4
replies
1.0k
views
How to extract genomic upstream region of a protein identified by its NCBI accession number?
bedtools extract_upstream_region genomic_sequence NCBI
2.6 years ago by mrj ▴ 170
3
votes
4
replies
1.8k
views
How can I extract upstream regions in fasta for all blastx hits locally performed on nr database?
fasta nr blastx upstream region
2.6 years ago by mrj ▴ 170
2
votes
2
replies
1.2k
views
How to pipe awk of bed file into samtools to extract fasta sequences?
bedtools pipe samtools bash
updated 2.6 years ago by ▴ 410 • written 2.6 years ago by ▴ 170
5
votes
4
replies
2.2k
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 15 days ago by 43k • written 2.7 years ago by ▴ 170
3
votes
2
replies
796
views
How to perform DESEQ2 analysis when there are three treatments (one of them being a reference)?
comparisons DESEQ2 expression multiple differential analysis
2.7 years ago by mrj ▴ 170
4
votes
2
replies
842
views
How to measure the similarity of operons from two species?
operon similarity bacteria
updated 2.9 years ago by ▴ 30 • written 4.0 years ago by ▴ 170
2
votes
2
replies
1.0k
views
How to map metatranscriptomics reads to a given genome (unannotated genome assembly)?
mapping genome alignment metatranscriptomics
2.9 years ago by mrj ▴ 170
2
votes
4
replies
1.1k
views
What are the disadvantages of increasing the sequencing depth of RNA-seq experiment?
NGS RNA-Seq sequencing depth transcriptome
3.1 years ago by mrj ▴ 170
2
votes
2
replies
1.8k
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 3.1 years ago by 141k • written 3.1 years ago by ▴ 170
1
vote
1
reply
828
views
Is genome coverage same as k-mer coverage for that genome?
genome coverage k-mer coverage
3.8 years ago by mrj ▴ 170
2
votes
2
replies
1.0k
views
reorder contigs into scaffold?
contig scaffold Assembly
updated 3.8 years ago by ▴ 230 • written 3.8 years ago by ▴ 170
0
votes
1
reply
833
views
How to interpret a contig statistics table?
Assembly WGS N50 contigs Soapdenovo2
3.8 years ago by mrj ▴ 170
1
vote
2
replies
800
views
How to detect different chromosomes from whole genome NGS reads of a fungi?
NGS scaffolds Assembly genome alignment
updated 4.2 years ago by ★ 3.8k • written 4.2 years ago by ▴ 170
4
votes
11
replies
1.6k
views
How to blastn a very short query sequence? Identifying telomeres in assembly
blastn blast shortquery telomere
updated 4.2 years ago by ▴ 20 • written 4.2 years ago by ▴ 170
5
votes
6
replies
1.3k
views
How to get a list of snp associated with any known cancer from NCBI with chromosomal locations?
SNP Cancer NCBI circos circularGenome
updated 4.3 years ago by ★ 1.2k • written 4.5 years ago by ▴ 170
0
votes
2
replies
1.9k
views
What are Metatranscriptomics databases?
metatranscriptomics metagenomics databases
updated 4.3 years ago by 3.6k • written 4.4 years ago by ▴ 170
32 results • Page 1 of 1
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