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User: colin.kern

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colin.kern • 810
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Posts by colin.kern

<prev • 112 results • page 1 of 12 • next >
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Comment: C: How to visualize narrowPeak file after peak calling using MACS?
... I agree with you, but the question wasn't "How should I visualize my ChIP-seq data" it was "How do I visualize a narrowPeak file" so I was just making it clear that the bedGraph file generated by -B is a different visualization showing slightly different information. ...
written 2 days ago by colin.kern • 810
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Comment: C: How to visualize narrowPeak file after peak calling using MACS?
... That will create a track of the normalized read pileups, but it won't show what peaks and peak boundaries were actually called by MACS2. ...
written 2 days ago by colin.kern • 810
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Comment: C: How to remove lines/headers from a SAM file after combined from different lanes
... UCSC browser is interpreting the file as being in the BED format, but Macs2 produces a file in narrowPeak format. The first 6 columns of both formats are the same, but the additional 4 columns that Macs2 produces are interpreted differently in a standard BED file. You can either tell UCSC that it is ...
written 7 days ago by colin.kern • 810
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Comment: C: How to visualize narrowPeak file after peak calling using MACS?
... Maybe. You didn't provide much detail about how exactly it isn't working, so I just had to guess what your issue might be. Are you getting an error message? If the problem is what I am guessing in my answer, you will probably not be getting any errors, but the track on the browser will be empty and ...
written 10 days ago by colin.kern • 810
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Answer: A: How to visualize narrowPeak file after peak calling using MACS?
... Your chromosome names are using the Ensembl identifiers. UCSC requires their own chromsome names to be used, which look like "chr1". You can convert the Ensembl ones to UCSC just by adding "chr" to the front, which works for all the main chromosome scaffolds. The unplaced/unlocalized ones aren't as ...
written 10 days ago by colin.kern • 810
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Answer: A: How to assemble viral genomes when my data contains host DNA as well
... If the host bacteria has a known genome assembly, you can use any short read aligner, e.g. BWA or Bowtie, to align your raw reads to the bacterial genome. Then take the unaligned reads and run your assembly pipeline just on those. ...
written 27 days ago by colin.kern • 810
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Answer: C: RNAseq read counts generated by FeatureCounts
... The read counts are not the average number per exon, they are close to the cumulative total, but not exactly because if a read spans a splice junction it would be counted as a read for two exons, but only contributes one count to the total gene count. ...
written 3 months ago by colin.kern • 810
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Answer: A: Thousands of significant differentially expressed genes but no significant enric
... > 1.) Is it possible to have no significant pathways despite having such a large fraction of the transcriptome being differentially expressed? > If so, what conditions would account for that? Yes, absolutely. Let's say, for easy math, that your species has 1000 genes and contains a pathway co ...
written 3 months ago by colin.kern • 810
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Comment: C: Want read count with respect to geneID instead of transcript IDs
... This might answer your question: https://www.biostars.org/p/119540/ ...
written 3 months ago by colin.kern • 810
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Answer: A: Want read count with respect to geneID instead of transcript IDs
... The default arguments for htseq-count will count by Ensembl gene ID. If you got read counts for Ensembl transcript IDs, I'm guessing your command has "-i transcript_id" in it. Remove that. If your GTF file doesn't use the attribute "gene_id" for gene IDs (GTFs downloaded from Ensembl should), you ne ...
written 3 months ago by colin.kern • 810

Latest awards to colin.kern

Popular Question 10 weeks ago, created a question with more than 1,000 views. For ChIP-seq Genome Coverage
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Quick Way to Annotate a Bed File
Scholar 3 months ago, created an answer that has been accepted. For A: How do I interpret genotype likelihood in the VCF format?
Scholar 3 months ago, created an answer that has been accepted. For A: How do I interpret genotype likelihood in the VCF format?
Centurion 3 months ago, created 100 posts.
Appreciated 3 months ago, created a post with more than 5 votes. For A: Effect of gene size on WGCNA
Scholar 3 months ago, created an answer that has been accepted. For A: How do I interpret genotype likelihood in the VCF format?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Quick Way to Annotate a Bed File
Scholar 3 months ago, created an answer that has been accepted. For A: How do I interpret genotype likelihood in the VCF format?
Popular Question 4 months ago, created a question with more than 1,000 views. For ChIP-seq Genome Coverage
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Quick Way to Annotate a Bed File
Scholar 7 months ago, created an answer that has been accepted. For A: How do I interpret genotype likelihood in the VCF format?
Scholar 7 months ago, created an answer that has been accepted. For A: How do I interpret genotype likelihood in the VCF format?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Quick Way to Annotate a Bed File
Popular Question 12 months ago, created a question with more than 1,000 views. For Tophat align_summary.txt and samtools flagstat accepted_hits.bam disagree
Popular Question 12 months ago, created a question with more than 1,000 views. For ChIP-seq Genome Coverage
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Quick Way to Annotate a Bed File
Scholar 13 months ago, created an answer that has been accepted. For A: Quick Way to Annotate a Bed File
Popular Question 15 months ago, created a question with more than 1,000 views. For Tophat align_summary.txt and samtools flagstat accepted_hits.bam disagree
Popular Question 15 months ago, created a question with more than 1,000 views. For ChIP-seq Genome Coverage
Popular Question 15 months ago, created a question with more than 1,000 views. For Scaffold name mapping between NCBI and Ensembl
Popular Question 18 months ago, created a question with more than 1,000 views. For Tophat align_summary.txt and samtools flagstat accepted_hits.bam disagree
Scholar 19 months ago, created an answer that has been accepted. For A: Quick Way to Annotate a Bed File
Great Question 24 months ago, created a question with more than 5,000 views. For Can't convert paired end BAM to bed using bedtools
Popular Question 24 months ago, created a question with more than 1,000 views. For vcf-consensus Error: Fasta sequence does not match REF
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