rnaseqr/RNASEQR — Issue #1: KeyError
Author: caddymob
Created: 2012-01-04 07:03:24+00:00
State: open

Hi there - really excited to try RNASEQR. I tested on some Rattus norvegicus data and get a key error. Can you help?

~/bin/python ~/bin/RNASEQR/RNASEQRp.py -q G2_62.R1.QC.fq.gz,G2_62.R2.QC.fq.gz rnaseqr.test.cfg

=== Sepicified Parameters ===
RNASEQR path: /users02/jcorneveaux/bin/RNASEQR
Aligner: Bowtie [/users02/jcorneveaux/bin/bowtie]
Mismatch: 0
Segment mismatch:1
Thread number:7
Phred: Sanger
Annotation: GTF [/scratch/jcorneveaux/RAT_iGenome/Rattus_norvegicus/Ensembl/RGSC3.4/Annotation/Genes/genes.gtf,/scratch/jcorneveaux/RAT_iGenome/Rattus_norvegicus/Ensembl/RGSC3.4/Annotation/Genes/Rattus_norvegicus.RGSC3.4.65.transcriptome]
Genome: [/scratch/jcorneveaux/RAT_iGenome/Rattus_norvegicus/Ensembl/RGSC3.4/Sequence/BowtieIndex/genome]
Maximum number of overlapping exons in annotation: [40]
Local aligner: /users02/jcorneveaux/bin/blat
Local aligner index: /scratch/jcorneveaux/RAT_iGenome/Rattus_norvegicus/Ensembl/RGSC3.4/Sequence/BlatIndex/genome.2bit
Input: G2_62.R1.QC.fq.gz,G2_62.R2.QC.fq.gz
Read Length: 50
Anchor-and-Map: Enabled
Anchor Length: 16
num_of_hit_anchor_to_be_valid: 2
Colorspace: False
==============================

Starting Preporcessing: Wed, 04 Jan 2012 07:01:04 +0000
KeyError: 1	protein_coding	exon	8276	8567	.	+	.	exon_number "2"; gene_id "ENSRNOG00000021490"; gene_name "LOC689435"; p_id "P21736"; transcript_id "ENSRNOT00000051735"; transcript_name "D3ZME0_RAT"; tss_id "TSS26275";

tmp_ENST,tmp_ENSG,tmp_exon_number ENSRNOT00000051735 ENSRNOG00000021490 2
{2: (8276, 8567)}