Hi
I am new to NGS and have a project to complete. The scenario is I have NGS (Illumina reads) from ants haploid brothers and a draft genome along with the linkage group. I need to find the TE( transposable elements) and the shared haplotype.
The logic i am thinking to work is :-
1. assess the quality of reads for the data
2. align the reads to the draft genome using BWA
3. Identify SNPs using SAMtools and use GATK to identify the shared haplotype
To identify the TEs I am planning to assemble the reads de-nove using SOAPdenovo and then use CENSOR or REPEAT MASKER to find the TE.
Please tell if my approach is right
In need to real and quick help.
Thanks
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