invalid feature coordinates from long read 'collapsed' assembly

gpertea / stringtie

Transcript assembly and quantification for RNA-Seq

MIT License

365 stars 76 forks source link

invalid feature coordinates from long read 'collapsed' assembly #338

Open noncodo opened 3 years ago

noncodo commented 3 years ago

So I 'collapsed' some long read data into a gtf with : /home/apps/stringtie2.1.4/stringtie ${BAMLIST} -p ${THREADS} -L -R -o hg38_merged.gtf I then try to quantify each sample/bam against this cleaned and collapsed reference, but get several

Error: invalid feature coordinates (end<start!) at line: chr1 StringTie exon 21220887 21220732 1000 - . gene_id "STRG.8348"; transcript_id "STRG.8348.1"; exon_number "1";

type messages. What's up with that? My bams are from minimap2.

xue-222 commented 1 year ago

Did you solve the problem?

noncodo commented 1 year ago

We manually remove the erroneous entries. Not an ideal solution.

On Apr 24, 2023, at 8:51 AM, xue-222 @.***> wrote:

Did you solve the problem?

— Reply to this email directly, view it on GitHub https://github.com/gpertea/stringtie/issues/338#issuecomment-1520098984, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABDCR3ZAKWEPEDTYFF3TY6TXCZZMJANCNFSM5CPEEMAQ. You are receiving this because you authored the thread.

xue-222 commented 1 year ago

Error: invalid feature coordinates (end<start!) at line: chr12 transcriptome mRNA 1197998703 1.198e+09 . + . ID=PtQG36900.3;Parent=PtQG36900 I made such an error, and I tried to convert scientific notation.