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User: colin.kern

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colin.kern • 300
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300
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Joined:
6 years, 6 months ago
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Posts by colin.kern

<prev • 58 results • page 1 of 6 • next >
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Comment: C: Differential Expression Analysis with batches which have different biological gr
... Since batch1 is only TypeA and there's no TypeA in any other batches, then it's theoretically impossible to distinguish differences that are true biological differences in TypeA from differences caused by a batch effect. ...
written 3 days ago by colin.kern • 300
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Comment: C: bedtools closest return no output!
... FYI bedtools can take GTF/GFF files instead of BED files, so there's not need to convert your GTF. As ATpoint said, if you show us the first few lines of each file it would help to figure out the error. ...
written 3 days ago by colin.kern • 300
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Answer: A: Questions related to ChromHMM+using MACS2 peak calling output bed file as input
... If you create your tissue marks file like this: Cell1 Mark1 Cell1_Mark1_Rep1.bam Cell1 Mark1 Cell1_Mark1_Rep2.bam Cell1 Mark1 Cell1_Mark1_Rep3.bam Cell1 Mark1 Cell1_Mark1_Rep4.bam Then ChromHMM will do the equivalent of combining all the bam files together. ...
written 16 days ago by colin.kern • 300
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Answer: A: bamCompare The best normalization for weak signal ChIP-Seq
... What SES is attempting to do is separate your background regions from your regions of enrichment, and only calculate the scaling factor based on the regions of enrichment. This is to avoid an issue with other scaling methods such as ones based on RPKM, where the scaling factor can be affected by the ...
written 16 days ago by colin.kern • 300
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Comment: C: Strand specification problem at deeptools (computeMatrix)
... What are the regions you're defining in your bed file that you use for the -R parameter? Can you edit your question and add a few lines from this file? ...
written 18 days ago by colin.kern • 300
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Comment: C: fastq file error
... Ok, the problem is that the ID and the sequence lines are being combined. ...
written 24 days ago by colin.kern • 300
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Comment: C: HTSeq count error while trying to read bam file
... That error is saying that a function is being called incorrectly. It's an error in the code, not in your input. This is probably being caused by incompatible versions of different python packages being installed. It can be pretty annoying to fix these kinds of issues, but reinstalling the software i ...
written 24 days ago by colin.kern • 300
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Answer: A: Downsampling single-end human ChIP-seq data
... > 1) How much you think I can downsample without having an unreasonable > coverage? Is 10M ok or given that is single-end more should be used? > (for example, in Girdhar et al 2018's schizophrenia chip-seq paper in > humans they used 13M but it was paired-end sequencing). The current EN ...
written 24 days ago by colin.kern • 300
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Answer: A: fastq file error
... Have you looked at your fastq file? Do you know what the fastq format should look like? It might help if you can update your question with the output of "head unmapped.fq". Every read in a fastq file is represented by 4 lines: @J00113:218:HGGJVBBXX:5:1101:27610:1226 1:N:0:NTTGTA ACCTATGAAAA ...
written 24 days ago by colin.kern • 300
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Comment: C: ChromHMM: chromatin states to genome % coverage?
... If you set up your tissue marks file to define each cell line separately, then ChromHMM should have produced segmentation files specific for each cell line. There should also be a file called CellLine_12_coverage.txt for each cell line, which has a genome coverage column. ...
written 25 days ago by colin.kern • 300

Latest awards to colin.kern

Scholar 19 days ago, created an answer that has been accepted. For A: How do I interpret genotype likelihood in the VCF format?
Scholar 24 days ago, created an answer that has been accepted. For A: How do I interpret genotype likelihood in the VCF format?
Teacher 24 days ago, created an answer with at least 3 up-votes. For A: Quick Way to Annotate a Bed File
Popular Question 5 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 5 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 6 months ago, created an answer that has been accepted. For A: Quick Way to Annotate a Bed File
Popular Question 8 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 8 months ago, created a question with more than 1,000 views. For ChIP-seq Genome Coverage
Popular Question 8 months ago, created a question with more than 1,000 views. For Scaffold name mapping between NCBI and Ensembl
Popular Question 11 months ago, created a question with more than 1,000 views. For Tophat align_summary.txt and samtools flagstat accepted_hits.bam disagree
Scholar 12 months ago, created an answer that has been accepted. For A: Quick Way to Annotate a Bed File
Great Question 17 months ago, created a question with more than 5,000 views. For Can't convert paired end BAM to bed using bedtools
Popular Question 17 months ago, created a question with more than 1,000 views. For vcf-consensus Error: Fasta sequence does not match REF
Popular Question 17 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 17 months ago, created a question with more than 1,000 views. For ChIP-seq Genome Coverage
Popular Question 17 months ago, created a question with more than 1,000 views. For Is combining fastq files before running tophat the same as combining bam file output from tophat?
Popular Question 17 months ago, created a question with more than 1,000 views. For Get # of unique mapped reads from Tophat output
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Is combining fastq files before running tophat the same as combining bam file output from tophat?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Get # of unique mapped reads from Tophat output
Student 2.7 years ago, asked a question with at least 3 up-votes. For Get # of unique mapped reads from Tophat output
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Can't convert paired end BAM to bed using bedtools
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Can't convert paired end BAM to bed using bedtools
Student 3.1 years ago, asked a question with at least 3 up-votes. For Get # of unique mapped reads from Tophat output
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Can't convert paired end BAM to bed using bedtools
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