im using strinTie as assembler for my project. and have got following warning messages. can anyone kindly help me to explain and resolve this issue ???
[05/18 14:00:48] Loading reference annotation (guides).. GFF warning: merging adjacent/overlapping segments of Cotton_A_18708_BGI-A2_v1.0 on chr1 (28601099-28601311, 28601314-28601385) GFF warning: merging adjacent/overlapping segments of Cotton_A_32496_BGI-A2_v1.0 on chr10 (65978961-65979005, 65979010-65979033) GFF warning: merging adjacent/overlapping segments of Cotton_A_27269_BGI-A2_v1.0 on chr8 (54954026-54954250, 54954253-54954306) GFF warning: merging adjacent/overlapping segments of Cotton_A_27269_BGI-A2_v1.0 on chr8 (54954026-54954306, 54954309-54954387)
the command line used is as follows:
./stringtie /data/memona/sorted.bam -v -p 60 -G /data/memona/genome.gff3 -C -A -o /data/memona/hisat_assembled_transcript2.gtf
thank you so much
You are using GFF annotation file while running strintie, but it is always better to use GTF file. Stringtie has issued a warning as there are overlapping segments in your GFF file.
thank you so much for the guidance. i have converted the GFF3 format to GTF and its giving the same warning.
is there any other possible solution???
would it effect the subsequent results as im interested to use it to determine Alternate splicing events???
Have you looked at your reference GFF file in IGV at the coordinates listed?
Can you give more information like, are these segments representing same feature or different?
what i have done is to align the RNA-seq data with Hisat2 and used that alignment to assemble the transcripts by stringtie and getting this warning. these two joined points are CDS of the same mRNA. the gene annotation file looks like this at these points:
kind help is need that would it effects the results????