I am analyzing paired end reads of several strains of a bacteria along with the ancestor.
Questions that I am trying to answer:
1. Which genes exhibited change between the ancestor and the 3 treatment groups of bacteria (5 replicates)?
2. Are the genes that have changed between ancestor and treatment groups similiar among the treatment groups?
So far this is what I have done:
1. FastQC - report overrepresented sequences
2. cutadapt - cut adapter sequences
3. BWA - map to reference
4. Picard - Process SAM files (Clean, BAM, Sort, MarkDup, AddReadGroups, Merge)
5. Call SNPs with SAMtools
I left off at step 5 and found the number of SNPs between the 3 treatment groups. But at this point I'm not sure what to do in order to answer my 2 questions.
I was told to use MUMmer. I tried to read the manual, but I have no idea what's going on.
Questions that I am trying to answer:
1. Which genes exhibited change between the ancestor and the 3 treatment groups of bacteria (5 replicates)?
2. Are the genes that have changed between ancestor and treatment groups similiar among the treatment groups?
So far this is what I have done:
1. FastQC - report overrepresented sequences
2. cutadapt - cut adapter sequences
3. BWA - map to reference
4. Picard - Process SAM files (Clean, BAM, Sort, MarkDup, AddReadGroups, Merge)
5. Call SNPs with SAMtools
I left off at step 5 and found the number of SNPs between the 3 treatment groups. But at this point I'm not sure what to do in order to answer my 2 questions.
I was told to use MUMmer. I tried to read the manual, but I have no idea what's going on.
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