Question: DE NOVO TRANSCRIPTOME AND COUNT
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ajmaninisha • 30 wrote:
Hi,
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 .
Please suggest
Thanks
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modified 3.1 years ago
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Jennifer Hillman Jackson ♦ 25k
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3.1 years ago by
ajmaninisha • 30
