bismark methylation extractor for PE reads
Rather than getting one single bam file, is it possible to get two separate bam files for reads F1 and R1 when your run bismark for a PE reads?
Can the following me modified accordingly?
bismark -p 4 -N 1 --path_to_bowtie /User1/NGS/ --samtools_path /User1/NGS/ --non_bs_mm --un --non_directional --ambiguous /User1/NGS/Library_1/ -1 Sample1_F1_P.fastq.gz -2 Sample1_R1_P.fastq.gz
Thank you all for your help!
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Out of curiosity, why would you want that?
The library I have is made up of <10 PCR amplicons for a ~2kb region of the genome. I want to be able to merge the F1&R1 reads from the two bam files (if I could generate them) to make a longer single read for each of the amplicons. Subsequently, I want to separate each amplicon in a unique file for each amplicon, to analyze them separately.
Alternatively, would it be possible to split the single bam file that I currently have into two files containing F1 and R1 reads which I could subsequently merge?
OR, could I do the merging of F1 & R1 reads without having to split the bam file?
Thank you!
But why do you want to merge the two reads to make a single read?
If you just want to separate each of your amplicons, you can filter the BAM file by coordinates.
Thanks, Igor I want to analyze DNA methylation change that happens within each amplicon. And be able to generate a figure accordingly for each amplicon.
I don't think you need to merge the two reads to make a single read. Just filter the BAM file by coordinates since you probably know those for each amplicon.
My interpretation is that NGS-Newbie really wants phased methylation status (presumably to make those closed/open circle style plots (do those have a name?) that you often see).
Exactly! With the NGS data, I can show a bigger picture. And using a uniform (smaller, say 5000 or 10000) number of amplicon-reads, I would like to be able to compare between samples to generate a figure.
I don't know if I remember those off the top of my head. Do you have an example?
Sure, here's an example:
Thanks! I have seen those. Not sure if there is a name for them.