How To Use Bwa For Multiple Reads Together With Reference Genome:

Question

[HG]

HI,i have 50 ecoli whole genome sequence reads. Now i want to align whole the data with reference genome. Can any one suggest some idea how to do it using bwa??

[Michael]

Please don't shout (all caps). Please read the bwa manual.

[HG]

Sorry for caps ....but i already gone through bwa manual . I find i can upload single genome but if i would like to multiple genome together then how i will do ?

[Michael]

sorry, I don't get what you want to do, and what have you tried? what do you mean by 'upload single genome'? what do you mean by 'to multiple genome together'?

[Ashutosh Pandey]

In case you have 50 different strains or genomes of Ecoli and you wish to align your reads against them, then you need to do it individually. I mean first align your reads against first genome. Then second and so on so forth.

[Sam]

Or it is possible to use tools like GSNAP which take into consideration of minor allele frequency while aligning. One of the colleague in my lab have tried to perform similar analysis. He first generated the gtf containing the difference between different strain of the same virus, then he aligned the reads using GSNAP. This allow him to use one single reference to align all our samples. The problem with this approach however is that it will require some more downstream processing to extract the strains information.

[Devon Ryan]

As Michael mentioned, your question, as posed, is ambiguous. Do you want to align reads against a genome, concatenate multiple genomes together and align reads against that, align multiple genomes to each other, or something completely different? The easiest thing would be to just tell us what your biological goal is and what you've done experimentally so far. Odds are good that we'll know better than you how to proceed given that information.