I am working with fastq files (paired reads) and with a reference genome. I need to do the mapping with STAR. I have done the index part and it's ok:
STAR --runThreadN 4 --runMode genomeGenerate --genomeDir /home/path/to/folder/ --genomeFastaFiles /home/path/to/genome_reference --readFilesCommand zcat samples.txt --sjdbGTFfile /home/path/to/genome_reference/annotation_file
However, when I try to run STAR for mapping
STAR --runThreadN 20 --genomeDir /home/path/to/folder/ --readFilesManifest /home/path/to/all_fastq_files/samples.txt
I used to have an error like this one:
Dec 03 12:55:45 ..... started STAR run Dec 03 12:55:45 ..... loading genome Dec 03 12:55:53 ..... started mapping EXITING because of FATAL ERROR in reads input: quality string length is not equal to sequence length @ST-E00494:118:HF3J7ALXX:7:2220:19593:58637 @ST-E00494:119:HF3GNALXX:6:1101:5457:11013 2:N:0:ACAAGCTA + SOLUTION: fix your fastq file Dec 03 14:03:44 ...... FATAL ERROR, exiting
Not sure what is happening. I have check the files (mainly the one that STAR indicates has an error) with FastQC but it look ok for me (size, umber of bases...).
Any idea how to fix this problem?
Thank you in advance