How the Galaxy bowtie wroks?

[tujchl]

I use Galaxy to analysis my chip-seq data and map reads by bowtie using default setting (In Galaxy leave "Bowtie settings to use" as defualt "most commonly used")

I found one of my reads:
@123
GGAAAATGATAAAAACCACACTGTAGAACATATTAG
+123
************************************
the mapping results is below:
123 16 chr6 103614979 255 36M * 0 0 CTAATATGTTCTACAGTGTGGTTTTTATCATTTTCC ************************************ XA:i:0 MD:Z:36 NM:i:0

as you see this read map to chr6 103614979

but I use blat to check the mapping quality (mm8/NCBI36): the blat outcome is below:
browser details YourSeq 36 1 36 36 100.0% 6 + 103614979 103615014 36
browser details YourSeq 36 1 36 36 100.0% 2 + 98463554 98463589 36
browser details YourSeq 36 1 36 36 100.0% 2 + 98467141 98467176 36

there are three perfect match which means this read is NOT unique match which can be fileterd. but bowtie give me no such information.
My question is commonly used option in Galaxy is so bad? or I miss some information?

[Dethecor]

See the bowtie manual

From the bowtie manual

Example 4: default (-k 1)

$ ./bowtie -v 2 e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT
- gi|110640213|ref|NC_008253.1| 148810 10:A>G,13:C>G
Leaving the reporting options at their defaults causes bowtie to report the first valid alignment it encounters. Because --best was not specified, we are not guaranteed that bowtie will report the best alignment, and in this case it does not (the 1-mismatch alignment from the previous example would have been better). The default reporting mode is equivalent to -k 1.

As you can see, this constitutes the default behaviour of bowtie and you can specify something else if you like.

Cheers,
Paul

[tujchl]

Thank you Paul
do you use galaxy? and if you do do you change parameter? and how do you change it?

[Dethecor]

Thank you Paul
do you use galaxy? and if you do do you change parameter? and how do you change it?

I personally don't use it, I tried it a couple of times though and think it's a very nice tool for automating your ngs pipeline.

When you use bowtie there is a field called "Bowtie settings to use" which will be set to "Commonly used" by default (at least for our galaxy it is). Switch that to "Full parameter list" and you should get a lot of options that you can configure amongst them those for reporting behaviour.

Cheers,
Paul

[tujchl]

One more question
I just switch -m to 1 in oder to get unique matching (at least I think so), Is it enough to get so?
what about your setting using bowtie? can you show it to me?

many thanks

[Dethecor]

Hi,

so I don't really use bowtie for alignment any more, last did so at least half a year back.

-m 1 should suppress reporting of reads with more than 1 alignment i.e. report only uniquely matching ones.

maybe you should throw in --best for good measure, though I would assumed that -m 1 implicitly includes --best, but that is something you might want to check yourself.

Cheers,
Paul

[tujchl]

thank you it helps me a lot