[dpryan]

You need to tell bowtie2 to ignore base qualities and then set the --score-min parameter accordingly (e.g., "--score-min L,-30,0 --ignore-quals" would allow a maximum of 5 mismatches).

[gongjing]

You need to tell bowtie2 to ignore base qualities and then set the --score-min parameter accordingly (e.g., "--score-min L,-30,0 --ignore-quals" would allow a maximum of 5 mismatches).

Hi dpryan,
thank you for your wonderful suggestion! But I am confused with the output while following your advise.
First,I use the command bowtie2 -x index/9402_ref_ASM32557v1_chrUn.fa -c ATGACAGGCTTATGTCGA -a --no-hd ,and the alignment result is

1 reads; of these:
1 (100.00%) were unpaired; of these:
0 (0.00%) aligned 0 times
1 (100.00%) aligned exactly 1 time
0 (0.00%) aligned >1 times
100.00% overall alignment rate
0 16 gi|584418266|ref|NW_006435781.1| 1491702 255 18M * 0 0 TCGACATAAGCCTGTCAT IIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:4T13 YT:Z:UU

then I tried the command: bowtie2 -x index/9402_ref_ASM32557v1_chrUn.fa -c ATGACAGGCTTATGTCGA --score-min L,-30,0 --ignore-quals -a --no-hd, but the aligning returns the same result, the --score-min L,-30,0 --ignore-quals seems not to help find more alignments with tolerated mismatchs. I also tried other sequence for input, but the field in XM:i:n returned is all XM:i:1 or XM:i:0(I think the field indicates the mismatch number). So is there any problem with my command ?

Sincerely.

[dpryan]

Firstly, there may not be any other valid hits with the specified number of mismatches. Secondly, even if there were, bowtie2 can miss alignments on occasion.