bowtie mapping report

[cascoamarillo]

Hi,

Maybe I'm missing some of the bowtie options, but when I map my reads against a pile of contigs (together in a reference file) and when I make the same mapping but only with one contig alone, I do obtain a different number of mapped reads ("reads with at least one reported alignment") for that contig. These are the options I normally use:

bowtie -f --sam --best

Any idea?

Thanks

[simonandrews]

This will be the result of having reads which could have been aligned to several different contigs. If you run the above command against all of them then the read will be assigned to the best alignment across all contigs.

If you run against just one contig then there will be reads which match well enough against that contig to be counted as a hit, but which matched better elsewhere and would have been reported there when searched against all of your contigs.

If you need to see consistency then you'd need to specify -m 1 as an option so that only reads with exactly one valid alignment would be reported, however this is a much more stringent search and your overall mapping efficiency would be reduced.

[cascoamarillo]

Hi Simon,

Thanks for the quick answer!
So if I want to do an alignment where there's no limit in the number of hits (-m has no limit) a read is reported (i.e., take each contig in the ref file as independent), should I take off the --best option? Or what do you recommend?

[simonandrews]

So if I want to do an alignment where there's no limit in the number of hits (-m has no limit) a read is reported (i.e., take each contig in the ref file as independent), should I take off the --best option? Or what do you recommend?

If you want to report multiple alignments you will need to increase -k (number of hits to report) to a suitably large value, and not set -m. We would normally then recommend running this in combination with --best and --strata which will ensure that all of the hits reported are equally good (ie same number of mismatches), so poorer valid hits are not reported if a better hit exists. This combination of options will still suffer from the effect you mentioned earlier where you won't get the same results from mapping against each contig individually compared to mapping against them all together.

If you really want to see every possible valid hit then you'd need to set -k to a high value, not set -m and not set either --best or --strata. This will produce consistent results (as long as you don't reach the limit for -k), but will also include sub-optimal hits when a better hit is found (eg you might see hits with 3 mismatches reported where there is also an exact match in your search set).

[oxydeepu]

i have a bowtie map output. as i am a newbie. i dont know what does the file designate..?? Does the file only have the aligned ones or does the report the unaligned formats also..?? Please help...

[simonandrews]

The default bowtie output will only show mapped sequences. The number of unmapped reads will be reported in the summary provided at the end of the run. You can optionally ask the program to write out a fastq file of the reads which didn't align by passing the --un parameter when you run the program.

[oxydeepu]

Thank you simon..
can you type me the rough commandline for that. i havent used the --un parameter yet.