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Using MapMan

RNAseq data ID

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RNAseq data ID
Answer
11/25/13 12:06 PM
Dear all,
I just started using mapman with RNAseq data from S. lycopersicum. I am not able create a data file suitable for mapman. I think the problem is the sample IDENTIFIER.
My sequences has been annotated and sequence names differs. Some examples:

TRNAY-GUA (chr11 3157240..3157334)
TRNAY-GUA (chr11 3159670..3159764)
TRNAY-GUA (chr11 33400015..33400098)
TRNAY-GUA (chr11 49123403..49123487)
TRNAY-GUA (chr11 5989605..5989700)
TRNAY-GUA (chr12 64274357..64274457)
TRNAY-GUA (chr3 44563578..44563669)
TRNAY-GUA (chr3 52883990..52884080)
TRNAY-GUA (chr4 4062830..4062913)
TRNAY-GUA (chr4 56205229..56205321)
TRNAY-GUA (chr4 57869442..57869529)
TRNAY-GUA (chr5 58949913..58949999)
TRNAY-GUA (chr6 41267790..41267876)
TRNAY-GUA (chr6 42762172..42762267)
TRNAY-GUA (chr7 60049701..60049794)
TRNAY-GUA (chr9 1793581..1793665)
TSI-1
TTS2
wee1
WRKY72
wus
XET4
XIP1-1-beta
XOPG1
XTH16
XTH6
XTH7
LOC101246400
LOC101262623
LOC101265380
LOC101249565
LOC101266713
LOC101266155
LOC544163
LOC101250637
LOC101250469
LOC101254806
LOC101259223
LOC101263732
LOC101265921
LOC544053
LOC101245049
LOC101248173
LOC101249115
LOC101251578
LOC101259704
LOC101247997
LOC101257192
LOC101255593
RBCS-2A

I tried to use marcator pipeline but I only have the raw reads files and it looks that the file is too big...

Any suggestion?

Thank you.

GC

RE: RNAseq data ID
Answer
11/25/13 12:19 PM as a reply to Giacomo Cocetta.
Dear Giacomo,

in order to be able to use MapMan, you need two files: The first is a mapping file that assigns the identifiers
you use to MapMan bins. Such a file can be generated by uploading the the protein or nucleotide sequences
to the Mercator tool (http://mapman.gabipd.org/web/guest/app/mercator). The other file is you actual data
file in which the first column has to contain the identifiers and all subsequent columns contain numerical
data for each of the identifiers. The identifiers used must be unique and identical to those in the mapping
file and should not contain spaces (maybe that's why you have problems).

To be able to help you better it would be necessary to know more details about what exactly you tried and
in what way that failed (e.g. error message issued by MapMan etc.)

Best greetings,
Marc