strand bias tools

[Mutagenic]

Does anyone know any tools for mapping regions of strand bias?

I want to simply create a bed file of regions where there is strand bias above or below a certain threshold.

[Apexy]

Hi,

What are you referring to by strand bias? Is this same as the mapping orientation? Do you wish to constrain reads so that they map to one strand and not the other?

[Mutagenic]

Hi,

What are you referring to by strand bias? Is this same as the mapping orientation? Do you wish to constrain reads so that they map to one strand and not the other?

Yes I am referring to strand orientation. Due to the assay, there is a disproportionate number of reads (only in particular regions) mapped in a single direction versus the other direction. This also affects the reads with called variants. There is bias towards a given strand in some cases. As a result some variants that are known variants are not called. I would like to map these regions so that I know how many potential regions/bases this affects.

[Apexy]

Hi Mutagenic,
I am aware that in bowtie, there is an option (--nofw/--norc) which can allows you do this type of thing but I have not used it. It is possible that other alignment tools might have a similar option.
Hope this helps!

[Sheila]

did you find a tool for strand bias calculatio ?

Yes I am referring to strand orientation. Due to the assay, there is a disproportionate number of reads (only in particular regions) mapped in a single direction versus the other direction. This also affects the reads with called variants. There is bias towards a given strand in some cases. As a result some variants that are known variants are not called. I would like to map these regions so that I know how many potential regions/bases this affects.

Hi,
I'm also trying to find a tool to obtain strand bias regions. Dealing with Sam file is quite tricky. Did you find any tool or perl/python library to do the job?
thanks very much in advance.
S.