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
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
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
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
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: