Bowtie2 result analysis

Question

[viswanathrana29]

Hi all, i am perform local alignment with bowtie2. the output is: -

17267759 reads; of these:
17267759 (100.00%) were unpaired; of these:
129533 (0.75%) aligned 0 times
8205103 (42.52%) aligned exactly 1 time
8933123(51.73%) aligned >1 times
99.25% overall alignment rate

i don't know it is right or not if it is right then how to analyse this, please help me. thank you

Answer 1

[Devon Ryan]

Without any context all anyone can say is that you got a nice alignment rate. Have a look at the alignments in IGV or something like that and see if they seem reasonable.

Edit: There's nothing to really analyse there. You have some summary metrics with nothing to compare them to.

Answer 2

[Sej Modha]

Could you please provide more information as to why you think this results is not right?

[viswanathrana29]

hi.. This Alignment are not classified in concordant or disconcordont. so i think...is it wrong alignment?

[Devon Ryan]

Were they paired end?

[viswanathrana29]

no..i have clean reads which are download from lotus database http://202.127.146.141/.so i perform local alignment

[Devon Ryan]

If you don't have paired-end data then there's no conception of "concordant" and "discordant" that could be quantified.

[viswanathrana29]

you mean it is right local alignment?

[Devon Ryan]

I'm sorry, "you mean it is right local alignment" can have too many meanings. If you mean, "So, does the output I posted from bowtie2 indicate that it likely ran correctly and to completion?", then yes.