Help with determine a closer-related genome

[pcmount87]

Hi,

I have a set of Illumina Hiseq 2000 bacteria transcriptome data set. From NCBI, I noticed that they have 2 same species but different strain genome sequence is available.

I decide to choose a closely related genome for my bacteria transcriptome data set as a genome-guide assembly.
Can I know how I determine which available genome is more closely related to my data set?

I have try to map the clean read of my bacteria transcriptome data set against those 2 genome separately.
It shown 97% of baceteria transcriptome read map to genome A (genome size is 4Mb) and 96% of bacteria transcriptome read map to genome B (genome size is 3.8Mb).
It seems like my reads map more in genome A than B.
But genome size of A is slightly larger than B.
I not sure whether more reads map to genome A is due to larger genome size in genome A.

Thanks for any advice that able to determine which genome is more closely related to my bacteria transcriptome data set.

[AdrianP]

Map reads to genome A as you did. The unused reads, map those to genome B. Do they map? Where and what genes?

Do the same with B, map to B, use unused reads to map to A, do they map? where?

Also, you got 2 strains of a bacteria, it is very likely that there is some significant difference between both. Perhaps an extra gene, or perhaps polymorphisms between the rRNAs. Look for those. Once you find something, look at your reads, which polymorphisms they have.

[pcmount87]

Hi AdrianP,

Many thanks for advice.

I will have a try based on your suggestion.
It is very useful for my research.
I have a try on it now.
Let you know once result is ready.

Thanks again, AdrianP.