xryanglab/RiboCode

Empty "transcripts_cds.txt" file

Opened this issue · 1 comments

huguanjing commented

Hi, the "transcripts_cds.txt" file generated is empty, how should I fix it? Thanks!

Here is GTF

A01	phytozomev13	gene	34694907	34695456	.	-	.	gene_id "Gohir.A01G126666.v2.1"; gene_name "Gohir.A01G126666.v2.1";
A01	phytozomev13	transcript	34694907	34695456	.	-	.	gene_id "Gohir.A01G126666.v2.1"; gene_name "Gohir.A01G126666.v2.1"; transcript_id "Gohir.A01G126666.1.v2.1";
A01	phytozomev13	exon	34694907	34695456	0	-	.	gene_id "Gohir.A01G126666.v2.1"; transcript_id "Gohir.A01G126666.1.v2.1"; Name "Gohir.A01G126666";
A01	phytozomev13	gene	119528395	119531897	.	+	.	gene_id "Gohir.A01G229700.v2.1"; gene_name "Gohir.A01G229700.v2.1";
A01	phytozomev13	transcript	119528395	119531897	.	+	.	gene_id "Gohir.A01G229700.v2.1"; gene_name "Gohir.A01G229700.v2.1"; transcript_id "Gohir.A01G229700.1.v2.1";
A01	phytozomev13	exon	119528395	119528785	0	+	.	gene_id "Gohir.A01G229700.v2.1"; transcript_id "Gohir.A01G229700.1.v2.1"; Name "Gohir.A01G229700";
A01	phytozomev13	exon	119528884	119529005	0	+	.	gene_id "Gohir.A01G229700.v2.1"; transcript_id "Gohir.A01G229700.1.v2.1"; Name "Gohir.A01G229700";
A01	phytozomev13	exon	119529125	119529262	0	+	.	gene_id "Gohir.A01G229700.v2.1"; transcript_id "Gohir.A01G229700.1.v2.1"; Name "Gohir.A01G229700";
A01	phytozomev13	exon	119529365	119529507	0	+	.	gene_id "Gohir.A01G229700.v2.1"; transcript_id "Gohir.A01G229700.1.v2.1"; Name "Gohir.A01G229700";
A01	phytozomev13	exon	119529601	119529736	0	+	.	gene_id "Gohir.A01G229700.v2.1"; transcript_id "Gohir.A01G229700.1.v2.1"; Name "Gohir.A01G229700";

And here is the script

(ribocode) [hugj2006@bigram2 translatome2022]$ prepare_transcripts -g td1.gtf -f ../cottonLeaf/refGenomes/TM1utx_26.fasta -o RiboCode_annot
[2022-06-08 05:12:58] Preparing annotation files ...
	Loading transcripts.pickle ...
[2022-06-08 05:13:09] The step of preparing transcript annotation has been completed.
(ribocode) [hugj2006@bigram2 translatome2022]$ 
(ribocode) [hugj2006@bigram2 translatome2022]$ ls -lh RiboCode_annot/
total 166M
-rw-rw-r--+ 1 hugj2006 domain users    0 Jun  8 04:53 transcripts_cds.txt
-rw-rw-r--+ 1 hugj2006 domain users  71M Jun  8 04:53 transcripts.pickle
-rw-rw-r--+ 1 hugj2006 domain users 186M Jun  8 04:53 transcripts_sequence.fa
zhengtaoxiao commented

There are no CDS regions in your GTF file. RiboCode infers the P-site based on the reads mapping to the known CDS regions.