Bowtie alignment report

[kevleb]

hello,

If someone can help me to understand bowtie (bowtie-0.12.7):
I have a pseudo-miRNA sequence with adaptor:
T01320202002122200123302010303131123
miRNAs - the base junction - adaptor


bowtie -t -C -f -S -k 10 --best --strata --col-keepends /share/reference/bowtie_index/hg19_c -c T013202020021222001
bowtie -t -C -f -S -k 10 --best --strata --col-keepends /share/reference/bowtie_index/hg19_c -c 13202020021222001
are exactly the same so i can understand and give me a good results :

chr4 143319992 18M CATCCTTCCCTGAGAAAC CM:i:0
chr19 54240159 18M TGCTTCCTTTCAGAGGGT CM:i:0
chr19 54264447 18M TGCTTCCTTTCAGAGGGT CM:i:0
chr19 54260055 18M TGCTTCCTTTCAGAGGGT CM:i:0
chr19 54228751 18M TGCTTCCTTTCAGAGGGT CM:i:0


Now:
bowtie -t -C -f -S -k 10 --best --strata /share/reference/bowtie_index/hg19_c -c 0132020200212220012


chr1 77836010 18M CAAAGCTGAAAGGAAGCA CM:i:1
chr3 7953493 18M GTTTCTCAGGGAACCTAC CM:i:1
chrX 40255290 18M CAGAAGGAAAGTCTCCCA CM:i:1
chr17 14643968 18M CATAAGGAAAGTCTCCCA CM:i:1
chr14 22781068 18M ACGAAGGAAAGTTCTTTG CM:i:1
chr7 42334833 8M CATCCTTCCCTTCTCCCA CM:i:1


If someone can explain me how it is possible ?
thanks

[kevleb]

Is there someone who can answer to this question ?
thanks.