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FastQ: quality string length is not equal to sequence length

I'm using starlong to map fastq reads according to the index (SB1003index2) created with star.

My code:

STARlong --quantMode GeneCounts --genomeDir SB1003index2 \ --readFilesIn all_DE.fastq \ --outFileNamePrefix DE_ \ --outSAMtype BAM SortedByCoordinate

My error: enter image description here

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!

star fastq starlong
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updated by GenoMax GenoMax • written by yvonnehhe • yvonnehhe

When I've had this error with STAR running seqkit sana resolved it, although this was for short read.

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written by rpolicastro rpolicastro

Thanks for the reply, I used seqkit sana but all the lines passed and it discarded 0 lines.

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written by yvonnehhe • yvonnehhe

If it can rescue a read it will do so without discarding it, so try realigning now to see if it worked.

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written by rpolicastro rpolicastro

Well, what does that entry look like in the fastq?

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written by swbarnes2 swbarnes2

Can you try aligning the data using minimap2? This may be a bug in STARlong.

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written by GenoMax GenoMax

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