I'm using starlong to map fastq reads according to the index (SB1003index2) created with star.
STARlong --quantMode GeneCounts --genomeDir SB1003index2 \ --readFilesIn all_DE.fastq \ --outFileNamePrefix DE_ \ --outSAMtype BAM SortedByCoordinate
I checked and the sequence and the quality scores have the same length (same number of characters).
I googled the error message, and someone suggested to remove all the run information after the first part of the identifier. I tried that but I'm still receiving the same error.
Any advice would be appreciated!