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Old 11-26-2009, 01:55 AM   #1
henry
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Default how bwa and bowtie handle repeats?

hg18 downloaded from ucsc consits of lower-case letters like a c g t.
human build 36 downloaded from ncbi consits of A C G T N.

Could anyone kindly tell me how bwa and bowtie deal with the Ns and lower-case letters when they map reads to the references?

Best
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Old 11-26-2009, 04:40 PM   #2
henry
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Bwa replaces Ns in the human genome from NCBI build 36 with A,C,G,T randomly. Bowtie by default excludes Ns.

As for hg18 in UCSC, there are lower-case letters for representing repeat regions in the genome. How do bwa and bowtie handle them?
Bwa replaces those lower-case letters with A,C,G,T randomly, or changes lower-cases letters into upper-cases first?

Bowtie excludes those lower-cases letters or changes lower-case letters into upper-cases first?

Hope someone can tell me.
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Old 02-03-2010, 12:18 AM   #3
KevinLam
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When gapped alignment is disabled, BWA is expected to generate the same alignment as Eland, the Illumina alignment program. However, as BWA change N in the database sequence to random nucleotides, hits to these random sequences will also be counted. As a consequence, BWA may mark a unique hit as a repeat, if the random sequences happen to be identical to the sequences which should be unqiue in the database. This random behaviour will be avoided in future releases.

Hope this helps
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Old 01-10-2011, 04:20 PM   #4
nashp
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Default I m lookin for the same answers

Hey
I am also looking for the same answers. What does 'n' in a read mean? in a genome mean? how is it handled in each of them by bowtie?

Please let me know if you have found answers to these

- Nash
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Old 01-20-2011, 11:30 PM   #5
louis7781x
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in bowtie ,use -m optioon ;for example, -m 2 means if output of alignment result >2 ,it's will print out "no alignment"
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Old 01-21-2011, 06:15 AM   #6
adamdeluca
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Quote:
Originally Posted by nashp View Post
Hey
I am also looking for the same answers. What does 'n' in a read mean? in a genome mean? how is it handled in each of them by bowtie?

Please let me know if you have found answers to these

- Nash
'n' means an ambiguous base call, an unknown. An N in a read is a mismatch, i.e. reported in the alignment as a T>N change for example. An N in the reference will cause the alignment to break (bowtie alignments can never span an N) the --ntoa option for building the index will convert all to A's so they can be treated as mismatches.
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Old 04-30-2014, 12:52 AM   #7
Liy
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Hi all,

Can someone please tell me, how exactly handle bowtie2 the multiple aligned reads? I ran the following commad and the results showed that ~50% of my reads (10m) could align multiple times.

bowtie2 -x ChIP_IP1.fastq.gz -S ChIP1_local.sam --very-sensitive-local --no-unal -p 6

Any suggestion, what to do with multi hits?

Thanky you!
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Old 04-30-2014, 03:52 AM   #8
mastal
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See the section of the Bowtie2 manual under the heading 'Reporting'

http://bowtie-bio.sourceforge.net/bo...html#reporting
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