It seems that falco doesn't handle reverse-complemented read sequences in mapped BAM files correctly.
Specifically, when flag bit 0x04 of a read is not set (i.e. when the read is mapped), falco should consider the status of the 0x10 bit and reverse-complement the sequence if that bit is set.
Example output of falco (multiqc visualized) on just the reverse-strand reads from a mapped bam:
and those same reads analyzed with fastqc:
It seems that falco doesn't handle reverse-complemented read sequences in mapped BAM files correctly.
Specifically, when flag bit 0x04 of a read is not set (i.e. when the read is mapped), falco should consider the status of the 0x10 bit and reverse-complement the sequence if that bit is set.
Example output of falco (multiqc visualized) on just the reverse-strand reads from a mapped bam:
and those same reads analyzed with fastqc: