Synthetic reads will have names like this:
@0_chr1_0_102714249_102714348_993561_chromosome_17
The first part can mostly be ignored. The important part is: "993561_chromosome_17"
This means it came from the sequence named "chromosome_17" and starts at position 993561 (zero-based). The end position is 993561-102714249+102714348=993660 (also zero-based). Note that in SAM files coordinates are listed as 1 based.
The reason the header is a little confusing is because the first part uses BBMap's internal coordinate system.
-Brian
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How do I get the true read origin information for each read generated by randomreads?
Thanks,
ilya
Synthetic reads will have names like this:
@0_chr1_0_102714249_102714348_993561_chromosome_17
The first part can mostly be ignored. The important part is: "993561_chromosome_17"
This means it came from the sequence named "chromosome_17" and starts at position 993561 (zero-based). The end position is 993561-102714249+102714348=993660 (also zero-based). Note that in SAM files coordinates are listed as 1 based.
The reason the header is a little confusing is because the first part uses BBMap's internal coordinate system.
-Brian