mitochondrial transcripts are ignored

[GoogleCodeExporter]

when loading a .gtf file mitochondrial transcripts are ignored.

is it possible to add an option to the annotation page in order to also
load these transcripts?

Original issue reported on code.google.com by mun...@gmail.com on 5 Aug 2009 at 2:33

[GoogleCodeExporter]

DIAGNOSIS: correct, in fact as a default chrM and haplotypes respectively random
chromosome fragments are filtered in the reader interface -- the intention has 
been
for simulation which uses the same reader interface. The chromosome names that 
are
filtered off are:

String[] DEFAULT_CHROMOSOME_FILTER = new String[] {
"^CHRM.*$", "^M$", "^MT$", "^U$", "^UN$", "^CHRU$", "^CHRUN$",
".*UNKNOWN.*", ".*_RANDOM.*",
".*_HAP.*", // chr5_h2_hap1
"^\\d{1,}H$", // droso, hetero?
"^CHR\\d{1,}H$", 
"^X{1}H$", "^CHRXH$", "^Y{1}H$", "^CHRYH$",
"^NT_.+$" }; // default chromosomes filtered off

This makes some sense in termes of gene expression, but not considering 
expression
prediction. I will deactivate any filtering for the Capacitor, and add more 
output to
the Simulator in the case of skipped chromosomes, expect a corresponding build 
in
around 1-2 working days. 

WORKAROUND: If you need a quick workaround -- just rename the chromosomes you 
want to
exclude from filtering to not match any of the above regular expressions, for
instance "foo".

STATUS: Bug remains open until final fixing reported. 

Original comment by gmicha@gmail.com on 5 Aug 2009 at 2:58

• Added labels: Capacitor

[GoogleCodeExporter]

Original comment by gmicha@gmail.com on 11 Aug 2009 at 9:08

• Changed state: Accepted

[GoogleCodeExporter]

All chromosomes from the input annotation are considered now by a corresponding 
call gtfReader.setNoIDs(null)
Remark: mappings from the mapped read file are to use the same nomenclature, 
e.g., the program will not consider reads that map to "chr6" for a gene 
annotated on a chromosome "chr6_hap1".

Original comment by gmicha@gmail.com on 21 Sep 2011 at 9:51

• Changed state: Fixed