Hi, I am new to this transcriptomic analysis stuff, so I apologize if my doubt is simple. I recently found that you can perform both mapping and counting with the --hisat2-hca parameter in RSEM, however I read that this works according to the Human Cell Atals SMART-Seq2 pipeline. Reading a little more I found that this is used for single cell RNA-seq, however the transcriptome I am analyzing is a standard RNA-seq, which generated me the doubt if this parameter can be applied in RSEM to perform the mapping and counting of transcripts to subsequently perform a differential expression analysis.
The command I plan to use is:
rsem-calculate-expression --paired-end --hisat2-hca --hisat2-path /usr/local/bin --paired-end -p 20 FH0_1_R1_T_PO.fastq.gz FH0_1_R2_T_PO.fastq.gz UniPAHC FH0_1_RHC &> FH0_1RH.txt
The RNA samples extracted followed the following experimental design: 24 samples in total, of which 12 belong to treated fruits and the other 12 a control, the effect of an inducer was evaluated at 0, 1, 24 and 72 hours in triplicate ( 4 times x 3 replicates = 12 samples).
Thank you very much in advance for your answer.
