  Baryon Acoustic Oscillations can be measured with sub-percent precision above
redshift two with the Lyman-alpha forest auto-correlation and its
cross-correlation with quasar positions. This is one of the key goals of the
Dark Energy Spectroscopic Instrument (DESI) which started its main survey in
May 2021. We present in this paper a study of the contaminants to the
lyman-alpha forest which are mainly caused by correlated signals introduced by
the spectroscopic data processing pipeline as well as astrophysical
contaminants due to foreground absorption in the intergalactic medium. Notably,
an excess signal caused by the sky background subtraction noise is present in
the lyman-alpha auto-correlation in the first line-of-sight separation bin. We
use synthetic data to isolate this contribution, we also characterize the
effect of spectro-photometric calibration noise, and propose a simple model to
account for both effects in the analysis of the lyman-alpha forest. We then
measure the auto-correlation of the quasar flux transmission fraction of low
redshift quasars, where there is no lyman-alpha forest absorption but only its
contaminants. We demonstrate that we can interpret the data with a
two-component model: data processing noise and triply ionized Silicon and
Carbon auto-correlations. This result can be used to improve the modeling of
the lyman-alpha auto-correlation function measured with DESI.
