FASTA file contains an unknown character error by rsem

Question

[LC]

RSEM produces "FASTA file contains an unknown character contains an unknown character, (ASCII code 13), at line XXX, position XXX" but not STAR during the indexing step. The problem has been mentioned elsewhere like https://groups.google.com/g/trinityrnaseq-users/c/BBvbInEQmLU/m/RqAM6k3MCgAJ?pli=1]

I solved my problem by:

1. sed -n "l" XX.fa to check the fa file
2. if you see \r in the file, you can use notepad++ to replace the \r with blank

[Pierre Lindenbaum]

f you see \r in the file, you can use notepad++ to replace the \r with blank

tr -d '\r' < xx.fa

[Malcolm.Cook]

dos2unix will edit in place such files