I am planning to generate reference de novo assembly as follow:
1] Creating reference assembly by pooling reads of all 6-samples i.e. WT and transgenic together in one fastq file.
2] Run velveth with auto parameter for K from 27 to 71 on that single fastq file
3] Afterword using velvethg for each value of K
4] Running oases on contig.fa file generated from each value of K
5] Transcript.fa file generated from each assembly are merged using Merged option in Oases
6] Checking merged assembly, by mapping each sample reads back to merged assembly using bowtie.
Am I on right path? Any suggestion would be appreciated.