Entering edit mode
6 months ago
yvonnehhe • 0
I'm using starlong to map fastq reads according to the index (SB1003index2) created with star.
STARlong --quantMode GeneCounts --genomeDir SB1003index2 \ --readFilesIn all_DE.fastq \ --outFileNamePrefix DE_ \ --outSAMtype BAM SortedByCoordinate
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!
When I've had this error with STAR running seqkit sana resolved it, although this was for short read.
Thanks for the reply, I used seqkit sana but all the lines passed and it discarded 0 lines.
If it can rescue a read it will do so without discarding it, so try realigning now to see if it worked.
Well, what does that entry look like in the fastq?
Can you try aligning the data using
minimap2? This may be a bug in