Reads aligned when using alignEndsType EndToEnd but not when set to Local

[Mario Keller]

Hi Alex,

I am currently testing alignment parameters. I have two sets of paramater settings that only differ by two parameters (  --outFilterMismatchNoverLmax and --alignEndsType):

Set1 uses  --outFilterMismatchNoverLmax 0.04 and --alignEndsType Local
Set2 uses   --outFilterMismatchNoverLmax 0.02 and --alignEndsType EndToEnd

I have a specific region of interest, where splicing takes place. It's an unannotated splice junction with a canonical intron motif (GT/AG). There are 8 uniquely mappable reads that support the splice junction. Using parameter setting 1 (so soft-clipping and more mismatches allowed) the reads are unmapped. However, when using parameter setting 2 (no soft-clipping and fewer mismatches allowed), the reads are perfectly mapped (without clipping and mismatches).

Do you have any idea why the reads are unmapped, when soft-clipping and more mismatches are allowed?

Thanks in advance.

Mario