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Using MapMan

Mercator works but data files don`t map back

Dear colleagues,

I work with orchid transcriptomes and used Mercator to create assignments for its differentially regulated genes. It worked, I was able to see the statistics and so on.

Then I try to visualize data on PageMan or Mapman and it dont work.


My .xls file contains ; ; ; and .

I don't know if have to add values from the three replicates of each sample, or if the problem is with identifiers identifiers. If anybody can help me to review this file. I tried many combinations of .xls file format but nothing works.

Kind regards,

Rafael Valadares


I am attaching my mercator file and two tables that I have tried to map.

Please any one ?

RE: Mercator works but data files don`t map back
Vastaus
10.2.2015 18:30 vastaus kirjoittajalle RAFAEL BORGES DA SILVA VALADARES.
To clarify my question. When looking into mercator.results file (in excel) I see that bin codes were assigned to my sequences, but I don`t see where the Uniprot identifiers are.

So it is likely that PageMan and Mapman cannot find coincidences between the data I enter (results file with Uniprot identifiers) and the mercator mapping (with bin codes and no longer uniprot identifiers). If anyone could clarify how to proceed.

regards,

Rafael.

RE: Mercator works but data files don`t map back
Vastaus
10.2.2015 18:36 vastaus kirjoittajalle RAFAEL BORGES DA SILVA VALADARES.
The problem are the identifiers in the FASTA file

e.g. you have sp|q9sgh4|pql2_arath in your mapping file
but want to map q9sgh4.

You can either resubmit or if it is always like this, split the identifiers in Excel.

Cheers
björn

RE: Mercator works but data files don`t map back
Vastaus
10.2.2015 18:42 vastaus kirjoittajalle Björn Usadel.
Dear Bjorn, but I can not figure out how can I correlate these identifiers. Results are allways like this.

I am re-submiting with only the Uniprot option selected.

RE: Mercator works but data files don`t map back
Vastaus
10.2.2015 19:00 vastaus kirjoittajalle RAFAEL BORGES DA SILVA VALADARES.
Uniprot is what it is mapped against as Mercator "knows" where uniport proteins should map to

your fasta file should like like this

>YOUR_ORCHID_IDENTIFIER_1 your annotation 1
SOMEPROTEINSEQUENCE1
>YOUR_ORCHID_IDENTIFIER_2 your annotatzion 2
SOMEPROTEINSEQUENCE2
>YOUR_ORCHID_IDENTIFIER_3
SOMEPROTEINSEQUENCE3

And your experiment file like this

IDENTIFIER EXPERIMENT1
YOUR_ORCHID_IDENTIFIER_1 -4.5
YOUR_ORCHID_IDENTIFIER_2 2.0
YOUR_ORCHID_IDENTIFIER_3 0.3


Mercator will then blast the sequence from YOUR_ORCHID_IDENTIFIER_1 against Arabidopsis, uniprort etc and
provide something like this
BINCODE NAME IDENTIFIER DESCRIPTION
1 Photosystem YOUR_ORCHID_IDENTIFIER_1 your annotation 1; many other things whcih Mercator figure out
1 Photosystem YOUR_ORCHID_IDENTIFIER_2 your annotation 2; many other things whcih Mercator figure out
4 Glycolysis YOUR_ORCHID_IDENTIFIER_3 things which Mercator figure out


So by default you should not change your sequence identifiers at all
Best
Björm

RE: Mercator works but data files don`t map back
Vastaus
10.2.2015 19:56 vastaus kirjoittajalle Björn Usadel.
Dear Bjorn. I understand completely but cannot figure out how to move on.

i) Fasta files has been build with uniprot identifiers (batch retrieve tool from uniprot site)

ii) Mercator files has different identifiers.

It is a pitty because this mapping should clarify and validate my results. MS is ready and waiting for this ... :/

many thanks


PS: I am attaching the fasta file (uniprot) used for mapping, if you could still help me, maybe to create mercator file. Don`t want to bother you.

RE: Mercator works but data files don`t map back
Vastaus
10.2.2015 20:11 vastaus kirjoittajalle RAFAEL BORGES DA SILVA VALADARES.
But didn't you say you have an orchid trqanscriptome?
>sp|A0SPJ9|NAM2_HORVD NAC transcription factor NAM-2 OS=Hordeum vulgare var. distichum GN=NAM-2 PE=3 SV=1
MGSSDSSSGSAPPRHQPPPPQQGSAPELPPGFRFHPTDEELVVHYLKKKAAKVPLPVTII
AEVDLYKFDPWELPEKATFGEQEWYFFSPRDRKYPNGARPNRAATSGYWKATGTDKPILA
SGCGREKVGVKXALVFYRGKPPKGLKTNWIMHEYRLTDASSSAATSRPPPVTGGSRAASL
RLDDWVLCRIYKKINKAAAADQQRSMECEDSVEDAVTAYPPYATACMTGEGAHGSNYASL
LHHQDSHEDNFLDGLLTAEDAGLSAGATSLSHLAAAARGSPAPTKQFLAPSSSTQFNWLD
ASTVGILPHARNFPGFNRSRNVGNMSLSSTADMAGAGTCAVDNGGGNAMNVMPPFMNHLP
VQDGTYHQQHVILGAPLAPEATGAAASAFQHPVQISGVNWNP

Is clearly barley.
The problem is here

>sp|A0SPJ9|NAM2_HORVD
is giving you
sp|A0SPJ9|NAM2_HORVD
as an identifier

and you seem to use A0SPJ9

So either you change
>sp|A0SPJ9|NAM2_HORVD NAC transcription factor NAM-2 OS=Hordeum vulgare var. distichum GN=NAM-2 PE=3 SV=1


to
>A0SPJ9 NAC transcription factor NAM-2 OS=Hordeum vulgare var. distichum GN=NAM-2 PE=3 SV=1

in the FASTA file

or you try changing this in the mercator file
if and only if you always need the second identifier you could something like this
=LEFT(MID(A7,FIND("|",A7)+1,LEN(A7)),FIND("|",MID(A7,FIND("|",A7)+1,LEN(A7)))-1)

from to

'sp|p10690|psbr_spiol' p10690
'sp|p80470|psby_spiol' p80470
'sp|q7dm39|psbp1_tobac' q7dm39
'sp|q8vy52|ppd2_arath' q8vy52
'sp|q9sgh4|pql2_arath' q9sgh4
'sp|q9tl00|psbd_nepol' q9tl00


but beware that excel likes to change e.g. 16.10 into 16.1 (avoid this by formatting as text and/or keeping quote)
(I jjust hacked this together but you shold look at all your ids in excel if this is your way to goi)

Best
Björn

RE: Mercator works but data files don`t map back
Vastaus
10.2.2015 20:28 vastaus kirjoittajalle Björn Usadel.
Yes, I understand. Do you know if there is any way to automate this changes in the fasta file ?

I tried also the command line to change the mercator file in excel and it didn`t work.

RE: Mercator works but data files don`t map back
Vastaus
10.2.2015 20:49 vastaus kirjoittajalle RAFAEL BORGES DA SILVA VALADARES.
Dear Bjorn, I finally dit it ! Many thanks, Rafael.