Use of custom schema in corona-lite pipeline

[npons]

I would like to fix "specific" positions for mismatches in reads before mapping. For example : for a 35bp long read : 2 random mismatches in the 20 first positions and 1 in the last 15 positions. I think it is possible with the -schema option but I didn't find any documentation about the use/construction of custom schema.

Thanks by advance for your help

[westerman]

I too have been frustrated by the lack of schema documentation. Also the seeming inconsistency of how the current schemas are constructed. They do not make much sense to me.

If you have not noticed, the schema creations seems to stem from Dan Gordon's site at http://www.ccrwest.org/cover/HIGH.html -- however I am afraid that I do not understand this site.

[david.lapointe]

I tried recreating a schema several times using data from the LJCR site and the design_to_schema_mapread.pl file. E.G. Using C(19,5,3) , referenced as the design file in schema_20_3 did not give a file which matched schema_20_3.

Does anyone have an idea how these are actually generated?

[drio]

I would like to fix "specific" positions for mismatches in reads before mapping. For example : for a 35bp long read : 2 random mismatches in the 20 first positions and 1 in the last 15 positions. I think it is possible with the -schema option but I didn't find any documentation about the use/construction of custom schema.

Thanks by advance for your help

I don't know if you want to stick to CL, but schema/index creation in bfast
is trivial. Give it a try if you can.

[aguffanti]

Schemas for rmapper

Hi - you should build something like that, even by hand, it is simple

111101111011111111111111101111111111
111110111110111111111111111110111111

.. etc ..

It is a mask (0 for mismatch, 1 for match), there is no way in which you can be more generic but you can put multiple schemas together

Probably a single perl script could produce these schemas for you ..


HTH

Alessandro

I would like to fix "specific" positions for mismatches in reads before mapping. For example : for a 35bp long read : 2 random mismatches in the 20 first positions and 1 in the last 15 positions. I think it is possible with the -schema option but I didn't find any documentation about the use/construction of custom schema.

Thanks by advance for your help