how bwa and bowtie handle repeats?

[henry]

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

[henry]

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.

[KevinLam]

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

[nashp]

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

[louis7781x]

in bowtie ,use -m optioon ;for example, -m 2 means if output of alignment result >2 ,it's will print out "no alignment"

[adamdeluca]

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.

[Liy]

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!

[mastal]

See the section of the Bowtie2 manual under the heading 'Reporting'

http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#reporting