Gene Expression Counts in Addition to Transposable Elements in a Count Matrix

bvaldebenitom / SoloTE

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Gene Expression Counts in Addition to Transposable Elements in a Count Matrix #27

Closed mitra-frn closed 9 months ago

mitra-frn commented 9 months ago

Hello, I have generated a count matrix that currently only includes transposable elements (TEs). However, I would like to expand this matrix to also include gene expression counts. In the related paper, it states that 'After annotating reads associated with TEs, a new matrix is obtained which incorporates both gene and TE expression per cell.' Could you please guide me on how to generate a count matrix that includes both known genes and TEs, as described in the paper?

bvaldebenitom commented 9 months ago

Hi,

did you check if your BAM file was generated using the following parameters in STAR?: --outSAMattributes NH HI nM AS CR UR CB UB GX GN sS sQ sM

Best, Braulio.

mitra-frn commented 9 months ago

Hi, You are right.I didn't include the GX GN sS sQ sM attributes in my STAR command.Thank you.