- I have done alignment using diamond with NR-DB. This step generated x.daa files , after that i have done megan using prot_acc2tax-May2017.bin. I have used paired end read mode for taxonomy analysis. This step generated y.rma file for me(Output–1 file). I have checked the read counts with respect to Bacteria and other kingdoms(i am interested in Bacterial counts).
- Because MEGAN do not support paired end mode for functional analysis, I have used x.daa files and meganized it with EggNOG mapping file (separately Read1 and Read2). This step generated data with respect to functions and i have exported it on CSV file. Additionally i have made a list of bacterial read counts for all x.daa files (Output—2 files).
3.Next i have extracted the bacterial reads from these x.daa files which has been eggnog mapped(Output–2 files).
Now i have compared the read counts with respect to bacteria for all above mentioned steps and each step give different read counts. How can this be possible. For your reference please have a look on below mentioned data:
Apart form this i am facing one another problem. The y.rma files provided read counts for archaea and viruses for all samples but x.daa files do not provide archaea and viruses read counts for all samples although the R1 and R2 for sample1 is same. Why it is happened.
Please help me out as soon as possible.