Hi Iris,
There is another potential issue I can think of which might cause such a low mapping percentage, and that is quite long reads paired with a high error rate.
As you are apparently using fasta sequences a Phred score of 40 is assumed for each base (making it impossible to look for base call error rates). If the sequencing run had a high error rate towards the end of the run you will potentially accumulate too many high quality mismatches which might result in the rejection of alignments. If this is the case you could try and raise the ceiling of cumulative mismatch scores (default 70) to 150 or so (-e 150). Alternatively you could trim the read length down to a value which should not have a high error rate, e.g. trim 100bp reads down to 50 or 60 bases which should be plenty to allow unique mapping.
Good luck!
There is another potential issue I can think of which might cause such a low mapping percentage, and that is quite long reads paired with a high error rate.
As you are apparently using fasta sequences a Phred score of 40 is assumed for each base (making it impossible to look for base call error rates). If the sequencing run had a high error rate towards the end of the run you will potentially accumulate too many high quality mismatches which might result in the rejection of alignments. If this is the case you could try and raise the ceiling of cumulative mismatch scores (default 70) to 150 or so (-e 150). Alternatively you could trim the read length down to a value which should not have a high error rate, e.g. trim 100bp reads down to 50 or 60 bases which should be plenty to allow unique mapping.
Good luck!
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