The command I used:
bowtie2 --fr -p 30 -x $GENOME -I 200 -X 800 -1 $READ1 -2 READ2 -S $SAM
I wanted to extract unmapped reads. When using samtools view -f0x4 I obtain unmapped pairs and pairs where one of the mates is mapped and the other is not mapped. In the latter case, both mates have a scaffold assignment. Second line, 69 flag --> read itself is unaligned.Looks like this is normal behavior however it is not intuitive at all.
7001253F:534:CBPYUANXX:1:1106:1173:2204#GTGAAA 137 scaffold1402 100976 42 43M = 100976 0 CTAGATTTTGACGATGGGAAAAGGAAAAAAATAAAGAAAAGAT B<BB/F<FFFFFF/FFFFFFFFFFFBFFFFFBBBB< 7001253F:534:CBPYUANXX:1:1106:1173:2204#GTGAAA 69 scaffold1402 100976 0 * = 100976 0 AACGTATTATACATATATATTATATATATATATGTGTATGTGTATATATATATATATATATATATAATGTTCTATACATAGAAC
My question is: Do you know why this is done? Is this a bug?