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Using MapMan

RNA-Seq: format file

RNA-Seq: format file
mapping file arabidopsis rna seq data input format file
Answer
10/19/13 4:08 PM
Hello folks,

I try to analyse my RNA-Seq data with MapMan, but I cannot generate the output.
I am not sure that I did something wrong

My input file (.txt) look like this

locus_name<tab>exp1<tab>exp2

AT1G01020<tab>1.021675<tab>0

AT1G01040<tab>0.610895<tab>0

AT1G01190<tab>-0.706153<tab>0


the mapping file that I use is 'Ath_AGI_ISOFORM_TAIR10_Aug2012'


I did many times but I still got nothing.

So, anybody has any idea about this

Best,
-Gib

RE: RNA-Seq: format file
Answer
10/19/13 5:03 PM as a reply to Gib Than.
Dear Gib

I reckon that it should work with the file indexed on locus (This are locus ids like AT1G01020)
whereas the isoforms have a .1 .2 .3 etc. to indicate different splice (or prediction isoforms) (e.g. AT1G01020.1 AT1G01020.2) in it.

Sorry for that inconvenience, but some of the .1 .2 .3 are actually really different and this is the way it is maintained by tair.
Pleas let me know if this doesn't fix your problems.

Best Wishes,
Björn

RE: RNA-Seq: format file
Answer
10/19/13 5:28 PM as a reply to Björn Usadel.
Dear Björn,

Thank you so much for your suggestion.

I changed the input file that specific the isoform of gene, but I still got nothing.
it likes no gene mapped to the database.

Best,
-Gib

RE: RNA-Seq: format file
Answer
10/19/13 5:46 PM as a reply to Gib Than.
Hi Gib

ok maybe we should have a look at the version.
I used the latest release candidate.
Then I added the data (the first column i configured as numeric the second as derived from the first (it looked like flags to me)
I opened Metabolism overview and when asked used the Mapping file
Ath_AGI_Locus_TAIR10_Aug2012.m02

In the pathway folder hovering over "metabolism_overview" it also shows me that link (if it doesn't righ click=> choose mapping)
on the map it tells me 3 of 3 data points mapped. 1 data point visible)

If this doesn't help maybe send me your file by email, so I can have a look at it and send you pcitures back.

Cheers,
b

RE: RNA-Seq: format file
Answer
10/19/13 6:17 PM as a reply to Björn Usadel.
Dear Björn,

Could you send me your email address?
Thank you so much emoticon

Best,
-Gib

RE: RNA-Seq: format file
Answer
10/19/13 6:23 PM as a reply to Gib Than.
sorry usadel AT bio1 DOT rwth-aachen DOT de