Hello everyone,
I am new at this but still trying to learn and work things out. I am assembling a genome and I mapped Nanopore reads to a reference genome. Does anybody can tell me or point me to a training to how extract mapped reads to a reference genome using Samtools?
Thank you!!
Hi @tigerlili
Two of the the Samtools suite tools are the top level descriptive statistics most people are interested in.
This one reports details from the perspective of the reference genome assembly input. What that reference is, and how many reads were mapped to each, along with some other details.
- Samtools idxstats reports stats of the BAM index file
Then this one reports details from the perspective of the reads input. You had sequences, but how many mapped or not, broken out into sub groups that the tools could detect.
- Samtools stats generate statistics for BAM dataset
This is a small history with a BAM file, then these two tools run with default settings, then both reports run through MultiQC to create a graphical view.
This is a nice tutorial to explore about mapping.
And this is a simple assembly tutorial that uses Nanopore reads.
Then if you search the tool panel with the keyword “samtools”, this will filter the tool listing. Click on any, and scroll down into the Help section for a brief summary (column headers, or links to content docs) plus other links to the tutorials that include the tool.
We were running a training event all week, and while it might be too late to join for the full program, the organization of the tutorials will remain online (and less overwhelming!). The Introduction then topic areas for Single Cell and Assembly might be worth reviewing. All of this will stay online indefinitely, including the videos. Scroll all the way down!
Good quesion! Hope this helps! 
Hi jennaj,
Yes, thank you very much for your input and guidance!!
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