Forum: De novo discovery
02-28-2012, 09:44 AM
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Replies: 82
Views: 42,869
Hi edge,
No sure what you are referring to...
Hi edge,
No sure what you are referring to in "Fail to get main class". You'll need to contact the support of the program you are using. If this is from CLC bio trial, write to...
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Forum: De novo discovery
02-27-2012, 08:14 PM
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Replies: 82
Views: 42,869
Hi Edge,
you may want to try the following: ...
Hi Edge,
you may want to try the following:
1. save the contigs created by each assembler in .fasta format. Or save just 1000 (or 100) longest contigs
2. download RefSeq proteins of your...
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Forum: De novo discovery
02-27-2012, 07:22 PM
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Replies: 82
Views: 42,869
How about BLASTX against RefSeq of related...
How about BLASTX against RefSeq of related species or group? I always wanted to see uninterrupted ORFs of expected size. I also always check for the presence of the longest transcript expected in...
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Forum: Events / Conferences
01-07-2010, 12:52 PM
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Replies: 5
Views: 3,760
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Forum: Events / Conferences
01-07-2010, 12:48 PM
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Replies: 5
Views: 3,760
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Forum: De novo discovery
12-16-2009, 09:22 PM
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Replies: 82
Views: 42,869
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Forum: De novo discovery
12-16-2009, 10:02 AM
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Replies: 82
Views: 42,869
KevinLam,
The data is unpublished. We are...
KevinLam,
The data is unpublished. We are re-assembling the reads using the latest version of CLC assembler and Velvet with adjusted parameters. The number of transcriptome contigs in our latest...
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Forum: De novo discovery
12-02-2009, 06:36 AM
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Replies: 82
Views: 42,869
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Forum: Sample Prep / Library Generation
11-28-2009, 04:34 PM
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Replies: 4
Views: 3,262
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Forum: Sample Prep / Library Generation
11-23-2009, 09:00 AM
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Replies: 7
Views: 9,818
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Forum: General
11-19-2009, 06:46 AM
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Replies: 14
Views: 13,575
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Forum: General
11-18-2009, 10:03 AM
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Replies: 14
Views: 13,575
simonandrews,
Thank you very much for your...
simonandrews,
Thank you very much for your posting. I did not experienced/realized this problem yet - the only way I used the indexes is by combining 12 libraries into one pool. In future I may...
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Forum: General
11-17-2009, 06:28 AM
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Replies: 14
Views: 13,575
I did not see any problems with analysis of...
I did not see any problems with analysis of unbalanced base composition. The main problem with pooling I experienced is unequal amounts of reads from different libraries in the pool. This is not...
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Forum: Bioinformatics
11-17-2009, 05:26 AM
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Replies: 236
Views: 516,582
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Forum: Bioinformatics
11-16-2009, 08:38 PM
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Replies: 236
Views: 516,582
Yes, CLC Genomics Workbench will use all three...
Yes, CLC Genomics Workbench will use all three data types. I use the program on Windows. However you will need lots of RAM. For my files/genomes I needed 32GB (the max we could put into my box). ...
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Forum: General
11-16-2009, 08:20 PM
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Replies: 14
Views: 13,575
I developed PE indexed adapters for our needs. ...
I developed PE indexed adapters for our needs. They worked fine w/o any special modifications, just 5'-P for all PE-1 adapters. We read the index as first 6 letters in each direction. The file can...
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Forum: Illumina/Solexa
10-23-2009, 10:35 AM
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Replies: 19
Views: 11,242
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