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8
votes
4
replies
338
views
How to merge set of bam files into one?
merge bam python pysam
updated 14 days ago by 38k • written 15 days ago by ▴ 130
3
votes
0
replies
338
views
Answer: Answer: How to merge set of bam files into one?
14 days ago by mrj ▴ 130
1
vote
1
reply
338
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Comment: Comment: How to merge set of bam files into one?
14 days ago by mrj ▴ 130
0
votes
1
reply
267
views
how to download NCBI partially non-redundant nucleotide dataset for prokaryotes?
NCBI dataset prokaryotes download nucleotide
updated 9 months ago by ★ 3.4k • written 9 months ago by ▴ 130
0
votes
0
replies
445
views
Comment: Comment: How to relate a categorical external trait (case, control) into WGCNA network?
11 months ago by mrj ▴ 130
1
vote
2
replies
445
views
How to relate a categorical external trait (case, control) into WGCNA network?
categorical eigen WGCNA gene relate
11 months ago by mrj ▴ 130
5
votes
3
replies
1.4k
views
How do I extract out ITS region from assembled whole genome sequence of a fungi?
genome Assembly alignment
updated 13 months ago by • 0 • written 3.8 years ago by ▴ 130
4
votes
4
replies
2.2k
views
why are all DiffBind tutorial's ATAC-seq peak intervals 400 bp for all intervals?
peak ATAC-seq intervals DiffBind consensus
updated 14 months ago by ★ 1.6k • written 16 months ago by ▴ 130
0
votes
0
replies
313
views
How to create motifs using biopython when the sequence object contain gaps (-)?
alphabet gaps motifs_create biopython
15 months ago by mrj ▴ 130
1
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1
reply
1.1k
views
Comment: Comment: How to identify the cell type computationally when you have a list of conserved
15 months ago by mrj ▴ 130
3
votes
3
replies
1.1k
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 15 months ago by ▴ 20 • written 15 months ago by ▴ 130
0
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0
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867
views
Comment: Comment: In single cell RNA-seq, do we perform regular quality checks and adapter trimmin
15 months ago by mrj ▴ 130
4
votes
2
replies
867
views
In single cell RNA-seq, do we perform regular quality checks and adapter trimming before using cellranger?
cellranger adapter_trimming QC scRNA-seq
15 months ago by mrj ▴ 130
0
votes
0
replies
2.2k
views
Comment: Comment: why are all DiffBind tutorial's ATAC-seq peak intervals 400 bp for all intervals
16 months ago by mrj ▴ 130
0
votes
1
reply
1.1k
views
Comment: Comment: How to import a BED file to ChIPseeker in order to visualize genome coverage plo
16 months ago by mrj ▴ 130
3
votes
3
replies
1.1k
views
How to import a BED file to ChIPseeker in order to visualize genome coverage plot?
ChIPseeker GRanges import ATAC-seq DiffBind
updated 16 months ago by ★ 2.3k • written 16 months ago by ▴ 130
0
votes
0
replies
606
views
Comment: Comment: How to check if a list of protein ID's are present in NCBI protein database?
16 months ago by mrj ▴ 130
2
votes
2
replies
606
views
How to check if a list of protein ID's are present in NCBI protein database?
esearch protein database NCBI
16 months ago by mrj ▴ 130
0
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0
replies
291
views
How to handle a esearch - elink empty result?
esearch ncbi protein elink
16 months ago by mrj ▴ 130
0
votes
0
replies
715
views
Comment: Comment: How can I export raw count profile from DiffBind to be analyzed on DESeq2 separa
16 months ago by mrj ▴ 130
2
votes
2
replies
715
views
How can I export raw count profile from DiffBind to be analyzed on DESeq2 separately?
raw DiffBind ATAC-seq profile export DESeq2 count
16 months ago by mrj ▴ 130
0
votes
0
replies
2.8k
views
Comment: Comment: How to parse cd-hit output (given in the description) to create a mapping file o
16 months ago by mrj ▴ 130
6
votes
5
replies
2.8k
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
16 months ago by mrj ▴ 130
2
votes
0
replies
2.8k
views
Answer: Answer: How to parse cd-hit output (given in the description) to create a mapping file o
16 months ago by mrj ▴ 130
0
votes
0
replies
2.8k
views
Comment: Comment: How to parse cd-hit output (given in the description) to create a mapping file o
16 months ago by mrj ▴ 130
0
votes
0
replies
767
views
Comment: Comment: What is a fast tool for searching sequence motifs in a large set of sequence fil
16 months ago by mrj ▴ 130
4
votes
2
replies
767
views
What is a fast tool for searching sequence motifs in a large set of sequence files?
search fast sequence motif
16 months ago by mrj ▴ 130
0
votes
0
replies
1.1k
views
Comment: Comment: How to use MACS2 output for DESEQ2 differential analysis during ATAC-seq? How to
16 months ago by mrj ▴ 130
1
vote
2
replies
1.1k
views
How to use MACS2 output for DESEQ2 differential analysis during ATAC-seq? How to get the intersect?
DESEQ2 ATAC-Seq intersect bedtools MACS2
16 months ago by mrj ▴ 130
0
votes
0
replies
647
views
Comment: Comment: How to extract two genomic location numbers within the following fasta header?
16 months ago by mrj ▴ 130
0
votes
0
replies
647
views
Comment: Comment: How to extract two genomic location numbers within the following fasta header?
16 months ago by mrj ▴ 130
2
votes
4
replies
647
views
How to extract two genomic location numbers within the following fasta header?
fasta extract location genomic bash
16 months ago by mrj ▴ 130
0
votes
0
replies
720
views
Comment: Comment: How to extract genomic upstream region of a protein identified by its NCBI acces
16 months ago by mrj ▴ 130
4
votes
4
replies
720
views
How to extract genomic upstream region of a protein identified by its NCBI accession number?
bedtools extract_upstream_region genomic_sequence NCBI
16 months ago by mrj ▴ 130
0
votes
0
replies
1.4k
views
Comment: Comment: How can I extract upstream regions in fasta for all blastx hits locally performe
16 months ago by mrj ▴ 130
0
votes
0
replies
720
views
Comment: Comment: How to extract genomic upstream region of a protein identified by its NCBI acces
16 months ago by mrj ▴ 130
3
votes
4
replies
1.4k
views
How can I extract upstream regions in fasta for all blastx hits locally performed on nr database?
fasta nr blastx upstream region
16 months ago by mrj ▴ 130
0
votes
0
replies
759
views
Comment: Comment: How to pipe awk of bed file into samtools to extract fasta sequences?
16 months ago by mrj ▴ 130
2
votes
2
replies
759
views
How to pipe awk of bed file into samtools to extract fasta sequences?
bedtools pipe samtools bash
updated 16 months ago by ▴ 320 • written 16 months ago by ▴ 130
0
votes
0
replies
1.4k
views
Comment: Comment: How can I extract upstream regions in fasta for all blastx hits locally performe
16 months ago by mrj ▴ 130
0
votes
0
replies
1.5k
views
Comment: Comment: How do we process Kallisto output (continuous real values) for DESEQ2 analysis (
18 months ago by mrj ▴ 130
5
votes
4
replies
1.5k
views
How do we process Kallisto output (continuous real values) for DESEQ2 analysis (which strictly require discrete count values)?
kallisto read DESEQ2 analysis counts differentialexpression
18 months ago by mrj ▴ 130
0
votes
0
replies
1.5k
views
Comment: Comment: How do we process Kallisto output (continuous real values) for DESEQ2 analysis (
18 months ago by mrj ▴ 130
1
vote
0
replies
585
views
Comment: Comment: How to perform DESEQ2 analysis when there are three treatments (one of them bein
18 months ago by mrj ▴ 130
3
votes
2
replies
585
views
How to perform DESEQ2 analysis when there are three treatments (one of them being a reference)?
comparisons DESEQ2 expression multiple differential analysis
18 months ago by mrj ▴ 130
4
votes
2
replies
650
views
How to measure the similarity of operons from two species?
operon similarity bacteria
updated 20 months ago by ▴ 30 • written 2.8 years ago by ▴ 130
0
votes
0
replies
749
views
Comment: Comment: How to map metatranscriptomics reads to a given genome (unannotated genome assem
21 months ago by mrj ▴ 130
2
votes
2
replies
749
views
How to map metatranscriptomics reads to a given genome (unannotated genome assembly)?
mapping genome alignment metatranscriptomics
21 months ago by mrj ▴ 130
0
votes
0
replies
906
views
Comment: Comment: What are the disadvantages of increasing the sequencing depth of RNA-seq experim
22 months ago by mrj ▴ 130
0
votes
0
replies
906
views
Comment: Comment: What are the disadvantages of increasing the sequencing depth of RNA-seq experim
22 months ago by mrj ▴ 130
68 results • Page 1 of 2
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