I have used STAR tool to align short read (150-160bp) transcript against hg38. Although, few suggested to use STARlong which resulted in increasing mapping percentage and mapped few transcripts as well. As STARlong used for long RNA reads. Therefore, It seems unfavourable to use for short reads. Kindly, suggest the possible solution or approach.

command line:

STAR --runThreadN 16 --runMode alignReads --genomeDir grch38_STARindex --readFilesCommand zcat --readFilesIn C_S30_1P.fastq.gz C_S30_2P.fastq.gz --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --outFileNamePrefix C_S30_

Output :

EXITING because of FATAL ERROR in reads input: quality string length is not equal to sequence length
    @A00573:363:HGYWYDSX7:2:2677:23728:19132
    +
    7:2:2654:20591:23594 24831472 N 0
    SOLUTION: fix your fastq file

    @A00573:363:HGYWYDSX7:2:2677:23728:19132
    +
    7:2:2654:20591:23594 24831472 N 0
    SOLUTION: fix your fastq file