How to solve STAR tools error : quality string length is not equal to sequence length ?

Question

[Aditya naman]

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

Answer 1

[GenoMax]

What program are you running that gives you this error?

In general it looks like your fastq file was corrupted in pre-processing. Tell us about what you did starting with original fastq data.

[Aditya naman]

Hey GenoMax, I have updated the details.

[GenoMax]

You will need to check C_S30_1P.fastq.gz C_S30_2P.fastq.gz using a fastq validation program such as fastqvalidator (LINK). If you have done nothing to these datafiles then perhaps they were corrupted during download from provider.

[Aditya naman]

I executed fastqvalidator in this file including others as well. As such no error was detected in the fastq file. So I guess the files are not corrupted at least.

[Aditya naman]

Hey GenoMax, Yes the files were corrupted. Thanks for the help.