I used STAR to assemble contigs for de novo transcriptomics data and used the following pipeline:
Assemble the reads by Star ---> use the assemble contigs as refernce and then map it to samples --> convert this sam file to fasta and blast it against own database to get the annoatations --->get the read count for mapped reads ---> and use edge R
Kindly advice am i using the right approach?
1) There are a number of discussions regarding counting reads for de novo assembly which one is the best ? cant i use htseq but that requires a gtf file .