getSpliced() error: improper genomic coordinate

Question

[tikshyadav19]

have searched through all the threads on this topic and I have yet to find a reasonable explanation for why I continue to encounter this error. I have already run Cufflinks on my samples, but when I attempt to run Cuffmerge

cuffdiff -o /scratch/sbag/Tikshana/BANANA/cuff/Macbal_diff -b /scratch/sbag/Tikshana/BANANA/RAW/Mac.fa -p 8 -u /scratch/sbag/Tikshana/BANANA/cuff/merged_asm/merged.gtf -L leaf,root /scratch/sbag/Tikshana/BANANA/map/Top_Macbal_6127/accept ed_hits.bam, /scratch/sbag/Tikshana/BANANA/map/Top_Macbal_6141/accepted_hits.bam

I get the following error:

Error (GFaSeqGet): end coordinate (46954453) cannot be larger than sequence length 46622217
GffObj::getSpliced() error: improper genomic coordinate 46954453 on chrUn_random for TCONS_00084296

PLEASE HELP ME TO CLEAR THIS…

[Bastien Hervé]

Seems like a read is mapped beyond a GTF feature. You have some info in here and there

In first instance try to remove -b option

[tikshyadav19]

Thank you all for your kind help. I simply want to suggest the future that if this sort of error will occur just check whether your input file is correct or not go through each and every location and check the path as well as your file name. Just keep everything simple do not complex anything. This is what I resolved these days. A small mistake in your command may hamper your time and experiment.

In short my bam file in samtools was not created properly so I run all command again and checked my path that resolved my issue/error. If you face the same just go through it make it SIMPLE