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1.5k
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Answer: A: ChIP-seq heatmaps using binding site of an specific protein as a reference
4.6 years ago by colin.kern ★ 1.1k
1
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1
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3.8k
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Comment: C: Are MACS2's summit or DiffBind's summit options are recommended for histone mark
4.7 years ago by colin.kern ★ 1.1k
0
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1
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3.3k
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Comment: C: low alignment rate with bowtie2 of ChIP-seq data 150bp pair end
4.7 years ago by colin.kern ★ 1.1k
1
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1
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2.8k
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Comment: C: H3K4me3 in promoter regions, which are free of nucleosomes
4.7 years ago by colin.kern ★ 1.1k
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0
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1.9k
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Comment: C: Is there a good way to do a PCA of gene expression including samples from differ
4.7 years ago by colin.kern ★ 1.1k
0
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1
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1.9k
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Comment: C: Is there a good way to do a PCA of gene expression including samples from differ
4.7 years ago by colin.kern ★ 1.1k
3
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9
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1.9k
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Is there a good way to do a PCA of gene expression including samples from different species?
RNA-Seq
updated 4.7 years ago by 82k • written 4.7 years ago by ★ 1.1k
2
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1
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962
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Answer: A: Dealing with spike-in reads that overlap between two genomes
4.7 years ago by colin.kern ★ 1.1k
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0
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1.9k
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Comment: C: Chip-seq H3k27 Bowtie2 Alignement
4.7 years ago by colin.kern ★ 1.1k
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1
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1.9k
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Comment: C: Chip-seq H3k27 Bowtie2 Alignement
4.7 years ago by colin.kern ★ 1.1k
1
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1
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1.2k
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Answer: A: In Peak Calling, what is the input sample
4.7 years ago by colin.kern ★ 1.1k
1
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2
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1.2k
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Answer: A: Chip-Seq Cancer Cell Lines
4.7 years ago by colin.kern ★ 1.1k
0
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0
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2.0k
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Comment: C: Amount of variants increased after bedtools subtract
4.8 years ago by colin.kern ★ 1.1k
0
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1
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671
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Comment: C: Coming from farm animal genomes, how do I deal with the large assemblies for mou
4.8 years ago by colin.kern ★ 1.1k
3
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3
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671
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Coming from farm animal genomes, how do I deal with the large assemblies for mouse and human?
alignment
4.8 years ago by colin.kern ★ 1.1k
1
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1
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2.3k
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Answer: A: Convert .bam.wig file to .bam file
4.8 years ago by colin.kern ★ 1.1k
0
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1
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1.9k
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Comment: C: Differential Expression Analysis with batches which have different biological gr
4.8 years ago by colin.kern ★ 1.1k
0
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0
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1.1k
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Comment: C: bedtools closest return no output!
4.8 years ago by colin.kern ★ 1.1k
1
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0
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3.8k
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Answer: A: Questions related to ChromHMM+using MACS2 peak calling output bed file as input
4.8 years ago by colin.kern ★ 1.1k
1
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0
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4.5k
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Answer: A: bamCompare The best normalization for weak signal ChIP-Seq
4.8 years ago by colin.kern ★ 1.1k
0
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0
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1.9k
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Comment: C: Strand specification problem at deeptools (computeMatrix)
4.8 years ago by colin.kern ★ 1.1k
0
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1
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2.7k
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Comment: C: fastq file error
4.9 years ago by colin.kern ★ 1.1k
0
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2
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2.0k
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Comment: C: HTSeq count error while trying to read bam file
4.9 years ago by colin.kern ★ 1.1k
4
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1
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2.8k
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Answer: A: Downsampling single-end human ChIP-seq data
4.9 years ago by colin.kern ★ 1.1k
0
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1
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2.7k
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Answer: A: fastq file error
4.9 years ago by colin.kern ★ 1.1k
0
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0
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3.2k
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Comment: C: ChromHMM: chromatin states to genome % coverage?
4.9 years ago by colin.kern ★ 1.1k
1
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0
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2.4k
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Comment: C: Question about ChromHMM overlap enrichment
4.9 years ago by colin.kern ★ 1.1k
0
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0
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2.0k
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Comment: C: macs2 callpeak results
4.9 years ago by colin.kern ★ 1.1k
6
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0
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3.8k
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Answer: A: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p
4.9 years ago by colin.kern ★ 1.1k
0
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0
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1.4k
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Error with NormR package using conda
R conda
4.9 years ago by colin.kern ★ 1.1k
3
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0
replies
2.5k
views
Answer: A: How do I interpret genotype likelihood in the VCF format?
5.3 years ago by colin.kern ★ 1.1k
4
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1
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2.5k
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How do I interpret genotype likelihood in the VCF format?
SNP vcf
5.3 years ago by colin.kern ★ 1.1k
0
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1
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1.6k
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Comment: C: How can I figure out the NCBI annotation version of a GFF file?
5.7 years ago by colin.kern ★ 1.1k
0
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5
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1.6k
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How can I figure out the NCBI annotation version of a GFF file?
rna-seq genome
5.7 years ago by colin.kern ★ 1.1k
1
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0
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1.8k
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Answer: A: Assessing chIP-seq plotfingerprint IP strength
5.8 years ago by colin.kern ★ 1.1k
6
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1
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7.4k
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Answer: A: Quick Way to Annotate a Bed File
5.8 years ago by colin.kern ★ 1.1k
0
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1
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1.1k
views
Finding SNPs between two inbred genetic lines
SNP
5.8 years ago by colin.kern ★ 1.1k
2
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3
replies
1.7k
views
Using UCSC Genome Browser with results from NCBI or Ensembl assemblies
ucsc browser ncbi ensembl
updated 6.3 years ago by 23k • written 6.3 years ago by ★ 1.1k
0
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0
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1.7k
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Comment: C: Using UCSC Genome Browser with results from NCBI or Ensembl assemblies
6.3 years ago by colin.kern ★ 1.1k
7
votes
12
replies
8.9k
views
6 follow
Split BAM file into two subsamples
alignment
updated 2.8 years ago by ▴ 140 • written 8.2 years ago by ★ 1.1k
1
vote
1
reply
4.0k
views
What exactly is the denominator when normalizing expression for sequencing depth?
RNA-Seq
updated 6.5 years ago by 104k • written 6.5 years ago by ★ 1.1k
6
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3
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5.7k
views
Why estimate fragment size of ChIP-seq with SPP when using Macs2 for peak calling?
ChIP-Seq
updated 7.2 years ago by 7.5k • written 7.2 years ago by ★ 1.1k
1
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0
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5.5k
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Answer: A: Please, please, define what a 'read' is.
7.5 years ago by colin.kern ★ 1.1k
0
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1
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7.9k
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Answer: A: ChIPseq - Identical peaks in IP and input samples
7.5 years ago by colin.kern ★ 1.1k
0
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1
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2.1k
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Comment: C: Does Cuffmerge discard single-exon transcripts?
7.7 years ago by colin.kern ★ 1.1k
1
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3
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2.1k
views
Does Cuffmerge discard single-exon transcripts?
cufflinks RNA-Seq
updated 7.7 years ago by ★ 1.6k • written 7.7 years ago by ★ 1.1k
0
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1
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3.1k
views
Count Unique Alignments in BAM file
RNA-Seq alignment
updated 7.7 years ago by 12k • written 7.7 years ago by ★ 1.1k
3
votes
2
replies
4.8k
views
Blastn doesn't allow certain gap penalties?
blast alignment
updated 18 months ago by 43k • written 8.7 years ago by ★ 1.1k
0
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0
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3.6k
views
Comment: C: vcf-consensus Error: Fasta sequence does not match REF
7.8 years ago by colin.kern ★ 1.1k
0
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3
replies
3.6k
views
vcf-consensus Error: Fasta sequence does not match REF
RNA-Seq vcf samtools software error
7.8 years ago by colin.kern ★ 1.1k
123 results • Page 2 of 3
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