STAR aligner FATAL ERROR not correct

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Entering edit mode

2.3 years ago

Mike ▴ 10

Hi, I downloaded a bunch of rna reads (mostly single-ends) and tried to align them to a reference genome using STAR aligner (without trimming!!).

Initially I got this error:

EXITING because of FATAL ERROR in reads input: quality string length is not equal to sequence length
@SRR9434783.1              
              TGGGAAATGACCCTCC..............

So I checked my fastq.gz file to see whether the reads had a sequence length that does not match the quality value string:

using zgrep -B4 -A8 "@SRR9434783.1" SRR9434783_1.fastq.gz I got tons of results, the first one:

enter image description here

The lengths are the same (701)

I downloaded the SRX's from NCBI. Is there a solution?

Thanks a lot.

fastq star • 844 views

ADD COMMENT • link updated 11 months ago by Ram 43k • written 2.3 years ago by Mike ▴ 10

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It seems your fastq data is very strange. The quality characters are not encodes following the widely-used Phred33 rule. So possibly STAR cannot recognize your quality line correctly. And, as far as I know, a read with 700bp is too long for next generation sequencing platform, like illumina. I wonder that your data is not a typical NGS data so that STAR cannot deal with it.

ADD REPLY • link 2.3 years ago by shiyang_bio ▴ 170

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You were right, STAR's author replied that it does not work well with long reads, he suggests using minimap2 or STARlong

ADD REPLY • link 2.3 years ago by Mike ▴ 10

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