Hi Jen:

I still have a little problem with the chromosome names. It appears that the 
mitochondria genes and chloroplast genes are named "ChrC" and "ChrM" in the 
gff3 file which I need to change to "chrC" and "chrM". How do I change cases 
specifically for the initial letters and not the entire words?

Thanks
Yang 

----- 原始邮件 -----
发件人: "Jennifer Jackson" <j...@bx.psu.edu>
收件人: "Yang Bi" <bey...@stanford.edu>
抄送: galaxy-user@lists.bx.psu.edu
发送时间: 星期一, 2014年 1 月 13日 下午 6:54:53
主题: Re: [galaxy-user] all FPKMs are 0 in the tmap files produced by cuffcompare

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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