Question on reads mapping to multiple genomes

[HenriettaHolze]

Hi Steven,

I'm wondering what reads classify as "One hit / multiple genomes" and "Multiple hits / multiple genomes".
Do you consider the mapping score or do you just count reads that are successfully aligned to both genomes within the allowed edit distance?
I would like to estimate how many reads I will be able to confidently assign to either genome using best mapping score and how many will be tied.

Thanks, Henrietta

[StevenWingett]

Hi Henrietta,

Thanks for your email. FastQ screen passes each read to BWA or Bowtie2 and, based on the mapping parameters, a read is considered to have mapped once, more than once, or not to have mapped.

The same reads are then passed to another genome and it is recorded once again whether a read maps once, more than once or not at all.

Thus we end up with a 1 / >1 / 0 value for read/genome combination. This is summarised in the FastQ Screen output.

I hope that answers your query.

Best, Steven