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1
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1.7k
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Answer: A: ChIP-seq heatmaps using binding site of an specific protein as a reference
5.2 years ago by colin.kern ★ 1.1k
1
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1
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4.3k
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Comment: C: Are MACS2's summit or DiffBind's summit options are recommended for histone mark
5.2 years ago by colin.kern ★ 1.1k
0
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1
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3.6k
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Comment: C: low alignment rate with bowtie2 of ChIP-seq data 150bp pair end
5.2 years ago by colin.kern ★ 1.1k
1
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1
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3.0k
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Comment: C: H3K4me3 in promoter regions, which are free of nucleosomes
5.2 years ago by colin.kern ★ 1.1k
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0
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2.0k
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Comment: C: Is there a good way to do a PCA of gene expression including samples from differ
5.3 years ago by colin.kern ★ 1.1k
0
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1
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2.0k
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Comment: C: Is there a good way to do a PCA of gene expression including samples from differ
5.3 years ago by colin.kern ★ 1.1k
3
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9
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2.0k
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Is there a good way to do a PCA of gene expression including samples from different species?
RNA-Seq
updated 5.3 years ago by 85k • written 5.3 years ago by ★ 1.1k
2
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1
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1.1k
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Answer: A: Dealing with spike-in reads that overlap between two genomes
5.3 years ago by colin.kern ★ 1.1k
0
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0
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2.1k
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Comment: C: Chip-seq H3k27 Bowtie2 Alignement
5.3 years ago by colin.kern ★ 1.1k
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1
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2.1k
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Comment: C: Chip-seq H3k27 Bowtie2 Alignement
5.3 years ago by colin.kern ★ 1.1k
1
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1
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1.3k
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Answer: A: In Peak Calling, what is the input sample
5.3 years ago by colin.kern ★ 1.1k
1
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2
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1.4k
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Answer: A: Chip-Seq Cancer Cell Lines
5.3 years ago by colin.kern ★ 1.1k
0
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0
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2.3k
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Comment: C: Amount of variants increased after bedtools subtract
5.3 years ago by colin.kern ★ 1.1k
0
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1
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737
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Comment: C: Coming from farm animal genomes, how do I deal with the large assemblies for mou
5.3 years ago by colin.kern ★ 1.1k
3
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3
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737
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Coming from farm animal genomes, how do I deal with the large assemblies for mouse and human?
alignment
5.3 years ago by colin.kern ★ 1.1k
1
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1
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2.5k
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Answer: A: Convert .bam.wig file to .bam file
5.3 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: Differential Expression Analysis with batches which have different biological gr
5.4 years ago by colin.kern ★ 1.1k
0
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0
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1.2k
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Comment: C: bedtools closest return no output!
5.4 years ago by colin.kern ★ 1.1k
1
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0
replies
4.2k
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Answer: A: Questions related to ChromHMM+using MACS2 peak calling output bed file as input
5.4 years ago by colin.kern ★ 1.1k
1
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0
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4.9k
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Answer: A: bamCompare The best normalization for weak signal ChIP-Seq
5.4 years ago by colin.kern ★ 1.1k
0
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0
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2.1k
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Comment: C: Strand specification problem at deeptools (computeMatrix)
5.4 years ago by colin.kern ★ 1.1k
0
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1
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3.1k
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Comment: C: fastq file error
5.4 years ago by colin.kern ★ 1.1k
0
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2
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2.2k
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Comment: C: HTSeq count error while trying to read bam file
5.4 years ago by colin.kern ★ 1.1k
4
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1
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3.1k
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Answer: A: Downsampling single-end human ChIP-seq data
5.4 years ago by colin.kern ★ 1.1k
0
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1
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3.1k
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Answer: A: fastq file error
5.4 years ago by colin.kern ★ 1.1k
0
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0
replies
3.4k
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Comment: C: ChromHMM: chromatin states to genome % coverage?
5.4 years ago by colin.kern ★ 1.1k
1
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0
replies
2.6k
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Comment: C: Question about ChromHMM overlap enrichment
5.4 years ago by colin.kern ★ 1.1k
0
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0
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2.2k
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Comment: C: macs2 callpeak results
5.4 years ago by colin.kern ★ 1.1k
7
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0
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4.3k
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Answer: A: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p
5.4 years ago by colin.kern ★ 1.1k
0
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0
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1.5k
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Error with NormR package using conda
R conda
5.5 years ago by colin.kern ★ 1.1k
3
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0
replies
2.7k
views
Answer: A: How do I interpret genotype likelihood in the VCF format?
5.8 years ago by colin.kern ★ 1.1k
4
votes
1
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2.7k
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How do I interpret genotype likelihood in the VCF format?
SNP vcf
5.8 years ago by colin.kern ★ 1.1k
0
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1
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1.7k
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Comment: C: How can I figure out the NCBI annotation version of a GFF file?
6.3 years ago by colin.kern ★ 1.1k
0
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5
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1.7k
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How can I figure out the NCBI annotation version of a GFF file?
rna-seq genome
6.3 years ago by colin.kern ★ 1.1k
2
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0
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2.0k
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Answer: A: Assessing chIP-seq plotfingerprint IP strength
6.3 years ago by colin.kern ★ 1.1k
7
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1
reply
8.1k
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Answer: A: Quick Way to Annotate a Bed File
6.3 years ago by colin.kern ★ 1.1k
0
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1
reply
1.1k
views
Finding SNPs between two inbred genetic lines
SNP
6.3 years ago by colin.kern ★ 1.1k
2
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3
replies
1.8k
views
Using UCSC Genome Browser with results from NCBI or Ensembl assemblies
ucsc browser ncbi ensembl
updated 6.9 years ago by 24k • written 6.9 years ago by ★ 1.1k
0
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0
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1.8k
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Comment: C: Using UCSC Genome Browser with results from NCBI or Ensembl assemblies
6.9 years ago by colin.kern ★ 1.1k
7
votes
12
replies
9.6k
views
6 follow
Split BAM file into two subsamples
alignment
updated 3.4 years ago by ▴ 140 • written 8.8 years ago by ★ 1.1k
1
vote
1
reply
4.1k
views
What exactly is the denominator when normalizing expression for sequencing depth?
RNA-Seq
updated 7.1 years ago by 104k • written 7.1 years ago by ★ 1.1k
6
votes
3
replies
6.0k
views
Why estimate fragment size of ChIP-seq with SPP when using Macs2 for peak calling?
ChIP-Seq
updated 7.8 years ago by 7.6k • written 7.8 years ago by ★ 1.1k
1
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0
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6.4k
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Answer: A: Please, please, define what a 'read' is.
8.1 years ago by colin.kern ★ 1.1k
0
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1
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8.6k
views
Answer: A: ChIPseq - Identical peaks in IP and input samples
8.1 years ago by colin.kern ★ 1.1k
0
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1
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2.2k
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Comment: C: Does Cuffmerge discard single-exon transcripts?
8.3 years ago by colin.kern ★ 1.1k
1
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3
replies
2.2k
views
Does Cuffmerge discard single-exon transcripts?
cufflinks RNA-Seq
updated 8.3 years ago by ★ 1.6k • written 8.3 years ago by ★ 1.1k
0
votes
1
reply
3.2k
views
Count Unique Alignments in BAM file
RNA-Seq alignment
updated 8.3 years ago by 12k • written 8.3 years ago by ★ 1.1k
3
votes
2
replies
5.1k
views
Blastn doesn't allow certain gap penalties?
blast alignment
updated 2.1 years ago by 44k • written 9.3 years ago by ★ 1.1k
0
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0
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3.8k
views
Comment: C: vcf-consensus Error: Fasta sequence does not match REF
8.3 years ago by colin.kern ★ 1.1k
0
votes
3
replies
3.8k
views
vcf-consensus Error: Fasta sequence does not match REF
RNA-Seq vcf samtools software error
8.3 years ago by colin.kern ★ 1.1k
123 results • Page 2 of 3
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