Determine mapping percentage from .fastq file

[SuzuBell]

Is it possible to obtain the mapping percent from .fastq file?

If I do the following:

grep "@HISEQ" -c file.fastq

I believe I obtain the number of sequences. Can this be used to determine the mapping rate without needing a .bam or .sam file?

[GenoMax]

No. Unless the data is mapped to a reference you would not be able to determine the mapping percentage. The % will change depending on the reference you use and/or options you choose for the aligner.

If for some reason you do not wish to create an alignment file you could use bbmap.sh from BBMap suite to get alignment statistics by not providing an "out=" file that would normally store the alignments. You can also sample a set fraction of reads (using "reads=1000000") option to get an idea of what the alignment percentage may be like.