User: johnsonn573

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Posts by johnsonn573

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Comment: C: Counting methylated and unmethylated CpGs in BSseq reads from bam file
... Thank you! This is very helpful! ...
written 16 days ago by johnsonn5730
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Answer: A: Counting methylated and unmethylated CpGs in BSseq reads from bam file
... I believe I found the answer to my question here. https://www.biostars.org/p/384127/ ...
written 16 days ago by johnsonn5730
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Comment: C: Counting methylated and unmethylated CpGs in BSseq reads from bam file
... Yes, I know how to do this, but I am not trying to extract methylation calls. See my other comment. ...
written 16 days ago by johnsonn5730
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Comment: A: Counting methylated and unmethylated CpGs in BSseq reads from bam file
... I know how to extract methylation calls using bismark. When you use bismark to call methylation, it will give you the number of methylated and unmethylated reads overlapping each CpG site in the genome. But that's not my question. I want to know all the methylated and unmethylated sites on each rea ...
written 16 days ago by johnsonn5730
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Counting methylated and unmethylated CpGs in BSseq reads from bam file
... I have a bismark aligned bam file, and I would like to extract the number of methylated CpGs and the number of unmethylated CpGs for each read in the bam file. ...
R sequence sequencing written 17 days ago by johnsonn5730
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GTF file problem
... I'm performing an RNA-seq analysis. I'm making a count matrix using bam files and a gtf file to make a count matrix. I wanted to compare my results using a gtf file from the hg19 (ftp://ftp.ensembl.org/pub/grch37/update/gtf/homo_sapiens/) build of the genome and the hg38 (ftp://ftp.ensembl.org/pub/ ...
gtf hg38 rna-seq hg19 written 24 months ago by johnsonn5730

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Scholar 16 days ago, created an answer that has been accepted. For A: Counting methylated and unmethylated CpGs in BSseq reads from bam file

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