I aligned many fastq files with HISAT2 to grch38. This proceeded without problems.
But in the next step with StringTie, which I am trying to find novel transcripts and their counts with the Gencode27 GTF:
stringtie Donor1_IL2OKT3ZA.HISAT2.sort.bam -G /illumina/runs/RNASeq/Gencode27/gencode.v27.annotation.gtf -A try.tab -p 4 > stringtie.out 2> stringtie.err
However, I get an error
WARNING: no reference transcripts were found for the genomic sequences where reads were mapped! Please make sure the -G annotation file uses the same naming convention for the genome sequences.
Why doesn't Stringtie recognize Gencode annotation? Do I have to do something to the gencode data?
Update: STAR works with this stringtie, but HISAT2 output doesn't. Strange.
stringtie's output from
cut -f 3 try.tab | sort | uniq
703404669@ssxfisctimga004:~/RNASeq_benchmark/GSE96075/HISAT2$ cut -f 3 try.tab | sort | uniq 1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 3 4 5 6 7 8 9 GL000008.2 GL000009.2 GL000194.1 GL000205.2 GL000214.1 GL000218.1 GL000219.1 GL000220.1 GL000221.1 GL000224.1 KI270442.1 KI270706.1 KI270711.1 KI270713.1 KI270721.1 KI270733.1 KI270734.1 KI270742.1 KI270744.1 KI270745.1 MT Reference X Y chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr2 chr20 chr21 chr22 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chrM chrX chrY
UPDATE: I have found several other instances of this error, but no one ever addressed how to solve this: