I have scRNAseq data and I am trying to use SplitNCigarReads on the bam files- I didn't do the alignment myself, I received these bam files from the scRNAseq provides. So far, everything has been ok (ie adding read groups, marking duplicates...) but now I have encountered this issue that SplitNCigarReads gives this error:
A USER ERROR has occurred: Badly formed genome unclippedLoc: Contig ERCC-00002 given as location, but this contig isn't present in the Fasta sequence dictionary
I am using GATK4.
My command is:
for fn in $(find /home/colpe/scratch/raw_data/marked_dup/ -name "*.bam")
gatk SplitNCigarReads -R /home/colpe/data/ref_sequences/Mus_musculus.GRCm38.dna.primary_assembly.fa -I "$fn" -O /home/colpe/scratch/raw_data/cigar_output/"$(basename $fn)"_sc.bam
I understand that there's an issue with ERCC-00002 - are these splice sites? What can I do about this?
Please sign in to leave a comment.