Can I use E. coli K strains reference for B strains Differential Gene Exp analysis?

[illuminaGA]

Dear All, I currently have a project for E. coli B strains Differential Gene Exp analysis. I did some search only found genome ref for K strains. So I am wondering Can I use E. coli K strains reference for B strains Differential Gene Exp analysis? Or just do a ref-free assembly?
Thank you so much.

[GenoMax]

You probably could, as long as the alignments work reasonably well and you use the same reference for all the samples being compared.

You were thinking of assembling the data otherwise and then using it as a reference?

[illuminaGA]

You probably could, as long as the alignments work reasonably well and you use the same reference for all the samples being compared.

You were thinking of assembling the data otherwise and then using it as a reference?

Thanks. I will try.

Yes, I was thinking about assembly the transcripts first based on the reference-free strategies.

[aprice67]

I recently published a paper on this exact topic. It show how alignment to non-native reference genomes influences outcomes and gives best practices for doing it. I used an e-coli data set in here too.

http://journals.plos.org/plosone/article/related?id=10.1371/journal.pone.0180904

I hope this helps, please let me know if I can help with anything!

[illuminaGA]

I recently published a paper on this exact topic. It show how alignment to non-native reference genomes influences outcomes and gives best practices for doing it. I used an e-coli data set in here too.

http://journals.plos.org/plosone/article/related?id=10.1371/journal.pone.0180904

I hope this helps, please let me know if I can help with anything!

Thank you so much. Let me digest the paper.

[aprice67]

Basically, to sum up, it's okay to use a non-native reference of a closely related strain as long as your reads are pretty long. Reads of 100bp do pretty well, 150 do great, 50 are bad. When you extract counts, be careful of edge cases, (see fig. 5 + 6), with htseq or featurecounts you can specify to avoid these false positives.

I'm happy to answer any specifics if have questions. Good luck!

[illuminaGA]

Basically, to sum up, it's okay to use a non-native reference of a closely related strain as long as your reads are pretty long. Reads of 100bp do pretty well, 150 do great, 50 are bad. When you extract counts, be careful of edge cases, (see fig. 5 + 6), with htseq or featurecounts you can specify to avoid these false positives.

I'm happy to answer any specifics if have questions. Good luck!

That great information, Thank you so much