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2 hours ago by

hi, I successfully aligned and analyzed my RNA-Seq data using Hisat2 and StringTIe and DESeq2 with the La_Amiga3_1 genome (white lupin) from NCBI to map transcripts. Beginner's luck. Now I am trying to do the exact same thing using the CNRS_Lalb genome (also white lupin on NCBI), and when I get to the first StringTIe step, I get "Error: no valid ID found for GFF record". I have looked at both the genome GTF files, and the first field (chromosome id) looks great (cut -f 1 *.gtf | sort | uniq) and they have a different name for the chromosomes, but look fine. I don't think that is the problem, and am looking for more hints as to what this means - I did read the StringTie manual but need more help. thanks very much,
K



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