Does it matters whether we give FASTA or FASTq files to STAR

Question

[rohitsatyam102]

Sorry! this is a nieve query!

I presume that since MAPQ quality is calculated while talking the base quality into consideration. What if we give fasta files to STAR aligner than FASTQ files. Does it affect the alignment scores assigned by STAR?

Answer 1

[swbarnes2]

Yes, but a fair amount of the mapping quality is determined by the nature of the sequence underneath; if your read maps to a sequence that is found in the genome 10 times, the mapq is never going to be good, no matter what your read quality is.

[rohitsatyam102]

So it does take Basequality into consideration. So saying this wouldn't be wrong that FASTQ files must be preferred over FASTA files?

[ATpoint]

Probably fastq is slightly preferred, and probably it does not make much of a difference either since as long as the sequencing was not super crappy most base qualities are anyway very high, and the longer the reads the less the base quality matters (I guess).