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
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