Gffread error: Error (GFaSeqGet): subsequence cannot be larger than...
Hello Biostars
I have a gtf annotation file produced by StringTie and a reference genome (fasta file). I am trying to use gffread to make a fasta file using the gtf file as reference for what sequences I want but I keep getting this error
Error (GFaSeqGet): subsequence cannot be larger than 225
Error getting subseq for MSTRG.51.1 (1..227)!
I know that all of the chromosomes are named appropriately and that this is the matching genome file. What else could I do to try to fix this error. I found many posts about this on the internet but they were all unanswered or due to differently named chromosomes, which I know is not a problem here. Thank you.
1 answer
Log in to answer this question.
More posts like this
-
Cannot Modify Fasta File description
written by bkffadia •
-
confusion about gffread extracting transcript sequence based on stringtie merge gtf
written by liyong •
-
Cufflinks de novo transcriptome assembly: genome indexing discrepancy causing assembly problems
written by Mason •
-
Multi-fasta file for gffread
written by vitor •
-
How to quantify gene expression when stringtie considers two adjacent genes as single gene?
written by kousi31 •
-
gffread error when extracting transcript sequences from gtf, coordinates exceed sequence length
written by jjrin •
-
Invalid reference '6L' even though naming of BAM files, fasta files, and gtf files are the same?
written by jjrin •
-
How to extract fasta sequences from assembled transcripts generated by Stringtie
written by seta
-
Cuffmerge error for large number of samples
written by Satyajeet Khare
-
About Cufflinks
written by Mayer fan •
