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Old 02-23-2009, 12:45 AM   #1
Blaize
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Location: Hungary, Vega 2kY Bioinformatics

Join Date: Jul 2008
Posts: 17
Default Abi Solid WT Sample Data vs. CLC Bio Genetics Workbench 3.0.0

Hi,

I'm just testing mRNA sequencing option of the CLC Genetics Workbench 3. Do you know any Abi Solid public data for it?

I have only two source: http://solidsoftwaretools.com/gf/dow...0_testData.tgz - but there isn't included qual file for proper importing it to CLC.

The other link is ftp://ftp.ncbi.nih.gov/pub/TraceDB/S...6_1_ES.tar.bz2 and ftp://ftp.ncbi.nih.gov/pub/TraceDB/S...6_2_EB.tar.bz2.
We succeed in importing, but setting annotated reference seqs failed.
We can download refseqs from ftp://ftp.ncbi.nih.gov/genomes/M_musculus/ in genbank format (*.gbk), importing to CLC is ok, but we can't choose them (one or multiple chromosomal gbk files) in the mRNA sequencing dialog. (http://www.clcbio.com/manual/genomic..._seq_step2.png) We can't see the imported refseqs at the list, where we can adding them to the analysis.

Alternatively I accept any kind NGS whole transcriptome public data (Roche 454 - sff./.fna/.qual or Illumina .txt /.fastq or Helicos (.fasta)

Thank you!
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Old 02-23-2009, 03:10 AM   #2
amhein
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Location: Denmark

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Default

Hi,
Genomics Workbench 3.0.0 only allowed (multiple) single sequences as input for the reference(s). However, the updated version, Genomics Workbench 3.0.1, allows list(s) of references sequences as input. You can download the updated version her:
http://www.clcbio.com/index.php?id=1294

Anne-Mette
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Old 02-23-2009, 03:44 AM   #3
Blaize
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Location: Hungary, Vega 2kY Bioinformatics

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Default 3.0.1

Yes, I'm just started it, it seems to works fine! Thnx!
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