Forum: Illumina/Solexa
10-06-2016, 07:19 AM
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Replies: 4
Views: 2,001
Yeah, that can for sure happen during the...
Yeah, that can for sure happen during the assembly processes, we've seen this during some comparative genomics tests.
But as suggested, use Pilon for error correction afterwards. It needs the reads...
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Forum: RNA Sequencing
10-06-2016, 07:14 AM
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Replies: 0
Views: 1,427
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Forum: RNA Sequencing
10-06-2016, 07:01 AM
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Replies: 4
Views: 2,212
Depending on the setup, 20% might also be...
Depending on the setup, 20% might also be acceptable.
What we've seen in some of our experiments is that, although the traces don't show any big peaks, we got a half ton of eukaryotic rRNA...
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Forum: Illumina/Solexa
10-06-2016, 06:54 AM
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Replies: 4
Views: 2,001
Miscalls in Illumina sequencing are not very...
Miscalls in Illumina sequencing are not very frequent, and should probably not be a consideration at this step.
As QC measure you can use the tool pilon for error correction afterwards.
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Forum: Bioinformatics
10-06-2016, 06:47 AM
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Replies: 12
Views: 16,417
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Forum: Bioinformatics
10-06-2016, 06:41 AM
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Replies: 3
Views: 1,461
I'd make DE all vs all, then sort out the...
I'd make DE all vs all, then sort out the statistically significant ones (no matter where they are significant) and do clustering on these (as suggested), to see which patterns are in there.
I...
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Forum: General
07-20-2016, 07:59 AM
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Replies: 3
Views: 1,723
I've for sure already cited the altschul paper...
I've for sure already cited the altschul paper ^^.
An appendix with the genomes/accession numbers sounds like a potentially good idea (although annoying) :).
But it's more about the citation. Do...
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Forum: Metagenomics
07-20-2016, 07:53 AM
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Replies: 3
Views: 3,820
Opera also scaffolds.
It might be...
Opera also scaffolds.
It might be recommendable to first to binning on the contigs and afterwards the scaffolding, because it might lead to better results (due to less ambiguous mapping within the...
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Forum: Metagenomics
07-20-2016, 07:47 AM
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Replies: 1
Views: 2,072
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Forum: Metagenomics
07-20-2016, 07:42 AM
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Replies: 3
Views: 2,578
Other things you'll need to do:
- assembly,...
Other things you'll need to do:
- assembly, best cross-assembly if you have multiple samples
- genomic binning (e.g. maxBin)
- gene prediction (prodigal has a setting for meta, but only bacteria;...
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Forum: Metagenomics
07-20-2016, 07:36 AM
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Replies: 11
Views: 3,281
Not sure if I get the question....you have...
Not sure if I get the question....you have reference genomes for all the bacterial data in your sample? And that then only 1 read of the PEs map to these genomes. That's how it sounds like for me.
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Forum: Bioinformatics
07-20-2016, 07:27 AM
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Replies: 4
Views: 2,029
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Forum: RNA Sequencing
07-20-2016, 07:22 AM
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Replies: 2
Views: 1,744
Why would the length matter? You should be...
Why would the length matter? You should be comparing the same gene between conditions (then the length doesn't matter). Comparing different genes in the same condition (where a length correction...
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Forum: Illumina/Solexa
07-20-2016, 07:16 AM
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Replies: 2
Views: 1,513
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Forum: General
07-20-2016, 07:11 AM
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Replies: 3
Views: 1,723
How do I cite a custom blast database?
Hi everyone,
I have a small problem.
I'm trying to finish writing a paper, and one of the remaining questions is how to deal with custom blast databases.
e.g. a simple thing: I use the human...
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Forum: Bioinformatics
01-13-2016, 06:09 AM
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Replies: 218
Views: 165,994
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Forum: Metagenomics
06-04-2015, 07:10 AM
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Replies: 5
Views: 3,149
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Forum: De novo discovery
06-04-2015, 07:03 AM
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Replies: 7
Views: 5,767
There are tools like CGAL and RSEM-EVAL, which...
There are tools like CGAL and RSEM-EVAL, which calculate the likelyhood of the reads belonging to the actual assembly. That might help when you're having more than 1.
Since sometimes the size of...
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Forum: Bioinformatics
06-04-2015, 06:57 AM
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Replies: 2
Views: 1,745
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Forum: Bioinformatics
06-04-2015, 06:52 AM
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Replies: 3
Views: 1,762
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Forum: Bioinformatics
06-04-2015, 06:46 AM
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Replies: 2
Views: 1,197
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Forum: Bioinformatics
06-04-2015, 06:41 AM
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Replies: 278
Views: 129,851
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Forum: Bioinformatics
06-04-2015, 06:21 AM
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Replies: 3
Views: 1,740
Sorry for the late answer, not regularly here. ...
Sorry for the late answer, not regularly here.
the iprlookup option will just look up if your protein has already been previously calculated at the EBI, and will return the results, which will also...
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Forum: RNA Sequencing
04-21-2015, 04:49 AM
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Replies: 2
Views: 1,668
No clue what the biological cause could be. ...
No clue what the biological cause could be.
What are your genes in this case? Protein coding sequences, or also noncoding RNA? If noncoding is included, does it also include noncoding besides tRNA...
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Forum: RNA Sequencing
04-21-2015, 04:44 AM
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Replies: 1
Views: 1,428
I don't think the differences in read length...
I don't think the differences in read length should matter too much (practical example: People do normalization with trimmed reads, they all have different lengths).
Because what you want is the...
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