Hi all.
I'm really new to sequencing.
I'm trying to map single end RNA-seq reads (short) to reference genome using (any) short read aligner. My question is, how do I find out if the program is mapping correctly using my data?
- input is some million reads of Ecoli K12 illumina RNA-seq data, 35bp in length
- ref is Ecoli K12 ~4.8MBp
- e.g. I use BWA 0.50 with bwtsw and it generated a sam file with position of each reads.
How do I know how correct the result in the SAM file is (statistically)? Or is there no way to find out and we have to trust result of correctness/ROC based on mapping known/simulated data (like this one?)
I'm really new to sequencing.
I'm trying to map single end RNA-seq reads (short) to reference genome using (any) short read aligner. My question is, how do I find out if the program is mapping correctly using my data?
- input is some million reads of Ecoli K12 illumina RNA-seq data, 35bp in length
- ref is Ecoli K12 ~4.8MBp
- e.g. I use BWA 0.50 with bwtsw and it generated a sam file with position of each reads.
How do I know how correct the result in the SAM file is (statistically)? Or is there no way to find out and we have to trust result of correctness/ROC based on mapping known/simulated data (like this one?)
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