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Forum: Bioinformatics 11-06-2015, 11:10 AM
Replies: 104
Views: 41,613
Posted By nepossiver
ok, noted. I will test on Illumina reads and...

ok, noted. I will test on Illumina reads and report back later. Many thanks.
Forum: Bioinformatics 11-06-2015, 05:45 AM
Replies: 104
Views: 41,613
Posted By nepossiver
How do you identify the mitochondrial band? Could...

How do you identify the mitochondrial band? Could you share the script?
Forum: Bioinformatics 05-27-2015, 08:10 AM
Replies: 2
Views: 902
Posted By nepossiver
You may do Differential Expression without...

You may do Differential Expression without replicates, and Trinity provides scripts for such case. However, you should not do so, if possible, because you will have low power and inflated false...
Forum: De novo discovery 05-13-2015, 08:41 AM
Replies: 7
Views: 5,154
Posted By nepossiver
Their (excellent, I love SPAdes and QUAST) group...

Their (excellent, I love SPAdes and QUAST) group is developing rnaQUAST (http://bioinf.spbau.ru/en/rnaquast), to evaluate transcriptome assemblies. Version 0.1.1 (current version at the time of my...
Forum: Bioinformatics 04-24-2015, 03:02 PM
Replies: 335
Views: 157,940
Posted By nepossiver
Thanks for the response, I understand your...

Thanks for the response, I understand your reasoning. I guess I could call bbduk twice to do a "two-pass" trimming, first trimming by minlen only, then adapters+minlen. As BBTools are so fast it does...
Forum: Bioinformatics 04-17-2015, 05:52 PM
Replies: 335
Views: 157,940
Posted By nepossiver
I've started to experiment with BBDuk, and I...

I've started to experiment with BBDuk, and I would like some help understanding the output. Initially I understood "KTrimmed" as the results of kmer adapter removal, but after playing a bit it seems...
Forum: Bioinformatics 04-08-2014, 11:27 AM
Replies: 0
Views: 1,670
Posted By nepossiver
What happened to the Forge Assembler?

I was looking at an Illumina technote from 2010 (De novo assembly using Illumina reads) and on that technote the assembler performing best for microbial genomes was Forge. However, it seems it does...
Forum: De novo discovery 10-12-2012, 01:03 PM
Replies: 7
Views: 5,154
Posted By nepossiver
hi ssing, how do you calculate chimeric...

hi ssing,

how do you calculate chimeric transcripts? Do you have a reference genome? My problem is, I don't, and I don't know of a good way to find chimeric contigs in my assemblies.

...
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