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Old 11-25-2016, 08:10 AM   #4
Zapages
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Quote:
Originally Posted by hamcan View Post
Thank you so much for your response! After I merge should I concatenate the unpaired files to the merged files? I'm running a BLAST to referenced bacterial genomes.
Another question, for removal of adapter sequences did I need the reverse complement sequences of the nextrra adapter sequences that were provided?
Thank you!
I would leave the unpaired files alone.

It all depends on what type of analysis are you trying to conduct?

If you are working on De-novo or novel assembled genomes.

Then the foremost step would be to do a de-novo assembly or do a reference guided assembly of your raw reads into contigs.

After contigs are formed then try to annotate them through BLASTX against a specific database of your choice ie. NCBI Bacterial database, NR Database, or a reference bacterial genome in your case.

If you are doing transcriptome analysis or a de-novo transcriptome analysis

De-novo Assemble your Raw Reads. Annotate your de-novo Assembled reads via BLAST just like mentioned above, and then map them against your reference genome or database of choice (NCBI NR database or Bacterial Database).

If its not a de-novo transcriptome analysis then just map them against your reference genome with the proper GTF/GFF3 files and settings.

Hope these strategies help.

Last edited by Zapages; 11-25-2016 at 08:12 AM.
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