Hello Yang,

Glad the problem was isolated - the mismatched chromosomes is definitely something to be fixed.


The tools in 'Text Manipulation" can help. The tool "Change Case of selected columns" can change the case for you. Click on the pencil icon after running the tool to reassign the datatype correctly as needed.

Take care,

Jen
Galaxy team

On 1/13/14 6:31 PM, Yang Bi wrote:
Hi Jen:

Thank you for the prompt reply. RPKMs produced by cufflink look normal (from an 
assembled transcript file):

Seqname Source  Feature Start   End     Score   Strand  Frame   Attributes
chr1    Cufflinks       transcript      11960   13178   1000    .       .       gene_id "CUFF.180"; transcript_id "CUFF.180.1"; FPKM 
"6.5441928094"; frac "1.000000"; conf_lo "3.594986"; conf_hi "8.987465"; cov "2.413218"; full_read_support 
"yes";
chr1    Cufflinks       exon    11960   13178   1000    .       .       gene_id "CUFF.180"; transcript_id "CUFF.180.1"; exon_number 
"1"; FPKM "6.5441928094"; frac "1.000000"; conf_lo "3.594986"; conf_hi "8.987465"; cov "2.413218";
chr1    Cufflinks       transcript      4536    5314    1000    +       .       gene_id "CUFF.178"; transcript_id "CUFF.178.1"; FPKM 
"11.0556332840"; frac "1.000000"; conf_lo "3.645830"; conf_hi "13.216134"; cov "4.076844"; full_read_support 
"no";
chr1    Cufflinks       exon    4536    4605    1000    +       .       gene_id "CUFF.178"; transcript_id "CUFF.178.1"; exon_number 
"1"; FPKM "11.0556332840"; frac "1.000000"; conf_lo "3.645830"; conf_hi "13.216134"; cov "4.076844";
chr1    Cufflinks       exon    4706    5095    1000    +       .       gene_id "CUFF.178"; transcript_id "CUFF.178.1"; exon_number 
"2"; FPKM "11.0556332840"; frac "1.000000"; conf_lo "3.645830"; conf_hi "13.216134"; cov "4.076844";
chr1    Cufflinks       exon    5174    5314    1000    +       .       gene_id "CUFF.178"; transcript_id "CUFF.178.1"; exon_number 
"3"; FPKM "11.0556332840"; frac "1.000000"; conf_lo "3.645830"; conf_hi "13.216134"; cov "4.076844";

I checked the chromosome names and I realized that the BAM outputs use lower cases for "RNAME", eg. 
"chr1" while my gff3 file uses initial capital letters for "seqId", eg "Chr1". Could this 
be the problem? What is the fastest way to convert the capital C in my gff3 file to lower case?

Thank you very much
Yang

--
Jennifer Hillman-Jackson
http://galaxyproject.org

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

 http://galaxyproject.org/search/mailinglists/

Reply via email to