Chimeric alignment with minimap2

Question

[Nicolas Rosewick]

Hi,

On minimap2 github (https://github.com/lh3/minimap2) it says :

For long RNA-seq reads, minimap2 may produce chimeric alignments potentially caused by gene fusions/structural variations or by an intron longer than the max intron length -G (200k by default). For now, it is not recommended to apply an excessively large -G as this slows down minimap2 and sometimes leads to false alignments.

How can I extract such chimeric reads ? Are these only cis-fusions (on the same chromosome) or also trans fusions (different chromosomes) ? Is there a way to tune the chimeric detection ?

Thanks

Answer 1

[Matteo Schiavinato]

If the output is a SAM-formatted file, you can retrieve them by including only reads that carry the 0x800 flag, using samtools view -f 0x800.

[xiaoleiusc]

is 0x800 flag we need in this case or SA tag we need in this case to filter chimeric alignments from Minimap2 results?