Question: Map on Koi genome (cyprinus carpio)
0
gravatar for n.gillet
4.0 years ago by
n.gillet0
Belgium
n.gillet0 wrote:

hi,

I would like to map reads onto the Koi genome (Cyprinus carpio), genome assembly deposited in the ENA under the projet code PRJEB7241, but I cannot find it on Galaxy. How can I do?

Best

nico

assembly bowtie • 1.3k views
ADD COMMENTlink modified 4.0 years ago by y.hoogstrate460 • written 4.0 years ago by n.gillet0
0
gravatar for Bjoern Gruening
4.0 years ago by
Bjoern Gruening5.1k
Germany
Bjoern Gruening5.1k wrote:

Hi Nico,

you can add against a FASTA file. This usually takes longer but if you only want to map against the genome I would map against a FASTA file.

Tata,

Bjoern

ADD COMMENTlink written 4.0 years ago by Bjoern Gruening5.1k

Thanks a lot best nico

Dr Nicolas Gillet Postdoctoral Researcher Molecular and Cellular Biology laboratory of Gembloux Agro-Bio Tech, 13 avenue Maréchal Juin, 5030 Gembloux - Belgium Molecular and Cellular Epigenetics, Interdisciplinary Cluster for Applied Genoproteomics (GIGA) of University of Liège (ULg), 1 avenue de l'Hôpital B34 Sart-Tilman, 4000 Liège - Belgium Tel: 0032(0)43 66 49 27 Mobile: 0032(0)485 76 74 24

ADD REPLYlink written 4.0 years ago by n.gillet0
0
gravatar for y.hoogstrate
4.0 years ago by
y.hoogstrate460
Netherlands
y.hoogstrate460 wrote:

Dear Nico,

As you might have observed in the article about the creation of these contigs, they did primary analysis only on the first 50 contigs (contig name "\t" size):

>gi|685042161|emb|LN590686.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG35 29126390
>gi|685042158|emb|LN590683.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG38 27918166
>gi|685042171|emb|LN590696.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG32 26100072
>gi|685042162|emb|LN590687.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG13 25164623
>gi|685042165|emb|LN590690.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG31 24603915
>gi|685042193|emb|LN590718.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG9 24322175
>gi|685042167|emb|LN590692.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG33 24142229
>gi|685042186|emb|LN590711.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG40 23490330
>gi|685042181|emb|LN590706.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG36 22739634
>gi|685042175|emb|LN590700.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG10 22665327
>gi|685042163|emb|LN590688.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG48 22470700
>gi|685042159|emb|LN590684.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG18 22437665
>gi|685042153|emb|LN590678.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG28 22269040
>gi|685042184|emb|LN590709.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG5 20922272
>gi|685042160|emb|LN590685.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG16 20606094
>gi|685042168|emb|LN590693.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG3 20567433
>gi|685042166|emb|LN590691.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG8 19797740
>gi|685042178|emb|LN590703.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG6 19716050
>gi|685042180|emb|LN590705.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG11 19054100
>gi|685042187|emb|LN590712.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG2 18998363
>gi|685042151|emb|LN590676.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG34 18891512
>gi|685042182|emb|LN590707.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG30 18521859
>gi|685042170|emb|LN590695.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG23 18435467
>gi|685042179|emb|LN590704.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG14 18393167
>gi|685042164|emb|LN590689.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG29 17515369
>gi|685042148|emb|LN590673.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG45 17310619
>gi|685042188|emb|LN590713.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG20 16766033
>gi|685042156|emb|LN590681.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG47 16759857
>gi|685042185|emb|LN590710.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG26 16349257
>gi|685042189|emb|LN590714.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG27 16295563
>gi|685042183|emb|LN590708.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG39 16255708
>gi|685042150|emb|LN590675.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG44 15901873
>gi|685042191|emb|LN590716.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG41 15851267
>gi|685042173|emb|LN590698.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG17 15849037
>gi|685042176|emb|LN590701.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG1 15297981
>gi|685042169|emb|LN590694.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG43 14329178
>gi|685042152|emb|LN590677.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG7 14157913
>gi|685042149|emb|LN590674.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG42 13570270
>gi|685042157|emb|LN590682.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG21 12985561
>gi|685042192|emb|LN590717.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG12 12725232
>gi|685042154|emb|LN590679.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG24 12449181
>gi|685042155|emb|LN590680.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG4 11347241
>gi|685042147|emb|LN590672.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG37 11248262
>gi|685042146|emb|LN590671.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG49 11140812
>gi|685042194|emb|LN590719.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG25 8535575
>gi|685042172|emb|LN590697.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG15 8518344
>gi|685042174|emb|LN590699.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG22 8395091
>gi|685042190|emb|LN590715.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG46 7828959
>gi|685042177|emb|LN590702.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG50 7653411
>gi|685042195|emb|LN590720.1| Cyprinus carpio genome assembly common carp genome ,scaffold LG19 7320473

You might want to think about this is well, since there are quite a lot of small contigs and indeed, carps are expected to have 50 chromosomes:

http://www.ncbi.nlm.nih.gov/pubmed/18464590

ADD COMMENTlink written 4.0 years ago by y.hoogstrate460
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