I have used Tophat2 and Hisat2 to align the RNASeq data. For Tophat2 I used Htseq-count to get read counts and calculate the TPM. While for Hisat2 I used StringTie, prepDE.py to read counts, to further calculated the TPM. But on comparing replicates, the correlation between Tophat2-TPM is higher than Hisat2. Although Hisat2 is now recommended over Tophat2, but due to poor correlation between replicates by Hisat2 I am confused which one to use for further analysis.
Attached is the link of correlation: https://www.dropbox.com/s/ixgfwo7ro4pwu42/Align.png?dl=0