FastQ: quality string length is not equal to sequence length

Question

[yvonnehhe]

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:

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!

[rpolicastro]

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

[yvonnehhe]

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

[rpolicastro]

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

[swbarnes2]

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

[GenoMax]

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