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
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viswanathrana29 •
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.
hi.. This Alignment are not classified in concordant or disconcordont. so i think...is it wrong alignment?
Were they paired end?
no..i have clean reads which are download from lotus database http://202.127.146.141/.so i perform local alignment
If you don't have paired-end data then there's no conception of "concordant" and "discordant" that could be quantified.
you mean it is right local alignment?
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.
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