Question: Sringtie gff output has "STRG." instead of genid
0
gravatar for morteza.khabiri
14 months ago by
USA/Ann Arbor/Biological Chemistry
morteza.khabiri10 wrote:

Hi all

I am trying to do genome assembly by stringtie software. The command that I am using is as follow:

  • " stringtie -p 2 -G dmel.gtf -o out.gtf STAR.bam "

  • The input bam file is from STAR.

The output file is look like this:

3R      StringTie       transcript      1       656     1000    -       .       gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "3.112805"; FPKM "382.908844"; TPM "572.137207";

3R      StringTie       exon    1       656     1000    -       .       gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "3.112805";

3R      StringTie       transcript      734     1776    1000    -       .       gene_id "STRG.2"; transcript_id "STRG.2.1"; cov "6.242569"; FPKM "767.903931"; TPM "1147.391479";

3R      StringTie       exon    734     1776    1000    -       .       gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "1"; cov "6.242569";

So as it shown above there is no "transcript_id" and "gene_id" corresponding to those in the input gtf file. Stringtie end with no Error so i can not understand what is wrong with my inputs.

Thanks

rna-seq assembly • 726 views
ADD COMMENTlink modified 14 months ago by genomax64k • written 14 months ago by morteza.khabiri10

See this: C: Help regarding RNA-seq STRINGTIE pipeline and output

ADD REPLYlink modified 14 months ago • written 14 months ago by genomax64k
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