rnaseqr/RNASEQR — Issue #3: Transcript IDs Not Found
Author: DarioS
Created: 2012-01-19 04:00:15+00:00
State: open

Even though my annotation file has the right transcript IDs, RNASEQR issues an error for every transcript anyway.

... ...
=== Sepicified Parameters ===
RNASEQR path: /home/darstr/tmp/source_codes
Aligner: Bowtie [/usr/local/bin/bowtie]
Mismatch: 3
Segment mismatch:1
Thread number:4
Phred: Illumina1.3
Annotation: GTF [/home/darstr/tmp/hg18Fixed.gtf,/home/darstr/tmp/mrnaInd]
Genome: [/usr/local/share/indexes/hg18/hg18]
Maximum number of overlapping exons in annotation: [40]
Local aligner: /home/darstr/bin/x86_64
Local aligner index: /gbdb/hg18/hg18.2bit
Input: /home/data/NGS_New/Ramaciotti/12-10-2010/s_2_1/s_2_1_sequence.fastq
Read Length: 76
Anchor-and-Map: Enabled
Anchor Length: 25
num_of_hit_anchor_to_be_valid: 2
Colorspace: False
==============================
... ...

Start Aligning: Thu, 19 Jan 2012 03:52:32 +0000
NM_003246 not in Your annoation.
FAIL in genome_GPS: ['GAPC:2:1:6877:1080#0/1', '0', 'NM_003246', '1102', '255', '76M', '*', '0', '0', 'TGGCCAATGAGCTGANGCGGCCTCCCCTATGCTATCACAACGGAGTTCAGTACAGAAATAACGAGGAATGGACTGT', "DGGDFGGDGG@3=@8#??<:=A9@>==8;
BB9;?:>A(;A#", 'XA:i:1', 'MD:Z:15G60', 'NM:i:1'] False
[] :: 1 :: []

... ...

darstr@clark-lab:~$ grep NM_003246 /home/darstr/tmp/hg18Fixed.gtf | head
chr15 unknown exon 37660572 37660721 . + . gene_id "THBS1"; transcript_id "NM_003246"
chr15 unknown exon 37661322 37661417 . + . gene_id "THBS1"; transcript_id "NM_003246"
chr15 unknown CDS 37661351 37661417 . + 0 gene_id "THBS1"; transcript_id "NM_003246"
chr15 unknown start_codon 37661351 37661353 . + . gene_id "THBS1"; transcript_id "NM_003246"
chr15 unknown CDS 37661686 37662245 . + 2 gene_id "THBS1"; transcript_id "NM_003246"
chr15 unknown exon 37661686 37662245 . + . gene_id "THBS1"; transcript_id "NM_003246"
chr15 unknown CDS 37663110 37663185 . + 0 gene_id "THBS1"; transcript_id "NM_003246"
chr15 unknown exon 37663110 37663185 . + . gene_id "THBS1"; transcript_id "NM_003246"
chr15 unknown CDS 37663481 37663680 . + 2 gene_id "THBS1"; transcript_id "NM_003246"
chr15 unknown exon 37663481 37663680 . + . gene_id "THBS1"; transcript_id "NM_003246"

Also, the error which appears underneath each annotation ID mismatch error - "FAIL in genome_GPS" etc etc - is uninformative to the end user.