Read strand

[sssxie]

I would like to know how to get the strand information of the read from nucleus.io.sam.SamReader, since I am working with bam files of long-read transcriptome.

[pichuan]

Hi @sssxie
Use this field:

nucleus/nucleus/protos/position.proto

Line 32 in 68d3947

bool reverse_strand = 3;

For example, in DeepVariant we use the strand information as one of our channels in our representation. Here is the C++ code that reads it: https://github.com/google/deepvariant/blob/c8fae5bd5f6c587bba733d83263a694aca252098/deepvariant/pileup_image_native.cc#L296

You can access the same field in the Python code as well once you have a Read.