Entering edit mode
7.2 years ago
NGS-Newbie
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10
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!
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.
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.
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.