Re: [galaxy-user] CuffDiff gene fpkm tracking file.

2011-02-03 Thread Jeremy Goecks 
 
 this is an example of my CuffDiff gene fpkm tracking file.
 
 tracking_id class_code  nearest_ref_id  gene_short_name tss_id  locus 
   q1_FPKM q1_conf_lo  q1_conf_hi  q2_FPKM q2_conf_lo  q2_conf_hi
 XLOC_01 -   -   MT-ND5  -   chrM:0-1657112484.2 
 12260.8 12707.7 11447   11233.1 11661
 XLOC_02 -   -   USP14   TSS1,TSS2,TSS3  chr18:148586-236453   
   16.7235 9.41244 24.0346 19.437  11.7368 27.1371
 XLOC_03 -   -   SMCHD1  
 TSS10,TSS11,TSS12,TSS4,TSS5,TSS6,TSS7,TSS8,TSS9 chr18:2719322-2728540   
 28.2493 17.5093 38.9892 27.2263 16.6263 37.8262
 XLOC_04 -   -   EMILIN2 TSS13,TSS14 chr18:2880607-2882469 
   3.98118 0   7.99721 4.62875 0.2785198.97899
 
 I this is normal, how can I find the class code of transcript listed in the 
 CuffDiff gene expression file?
 


Hi Samuele,

Without seeing your history, it's difficult to say for certain what your 
problem is. However, I'd guess that the GTF file that you're providing to 
Cuffdiff does not have the p_id attribute. You can produce a GTF file with both 
tss_id and p_id attributes by running Cuffcompare and using sequence data.

Thanks,
J.
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Re: [galaxy-user] FASTQ collapse?

2011-02-03 Thread Ben Bimber 
 and
  configuration steps (sometimes can be difficult) if you want to run a 
  local Galaxy
  instance.
 
  If you are interested in this procedure or have questions on that, we are 
  happy to
  share our experience and scripts.
 
  Best regards,
  Leon
 
  --
  Hailiang (Leon) Mei
  Netherlands Bioinformatics Center (http://www.nbic.nl/)
  Skype: leon_mei? ? Mobile: +31 6 41709231
 
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 Message: 7
 Date: Thu, 3 Feb 2011 12:51:34 -0500
 From: Johnson, Kory (NIH/NINDS) [C] johnso...@ninds.nih.gov
 To: 'galaxy-u...@bx.psu.edu' galaxy-u...@bx.psu.edu
 Subject: [galaxy-user] FASTQ collapse?
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 Hello,

 Is there an option to collapse duplicate sequences in FASTQ format.

 I see collapse for FASTA, but where is it for FASTQ?

 Thank you,

 Kory

 

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Re: [galaxy-user] FASTQ collapse?

2011-02-03 Thread Johnson, Kory (NIH/NINDS) [C] 
 information in error, please notify the sender immediately by 
 telephone.  Thank you.

 

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