I am trying to assemble RNA transcripts using stringtie and facing the following error.
Error parsing strand (?) from GFF line: NC_037304.1 RefSeq gene 58315 59481 . ? . ID=gene-DA397_mgp34;Dbxref=GeneID:36335702;Name=nad1;exception=trans-splicing;gbkey=Gene;gene=nad1;gene_biotype=protein_coding;locus_tag=DA397_mgp34;part=2
my comand is :
stringtie -p 8 -G Genome/arab_thaliana.gtf -o Assemble/NR1.gtf –l NR1 NR1.bam
One solution I could think of is to remove the lines where strand has '?' but just thinking that I may miss any important information / transcript ?? If someone could guide me regarding this ??
if you want to get information from strand=? lines, probably you will need to manually assess them somehow so filtering them to a separate file may be helpful