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Forum: De novo discovery 05-30-2013, 11:37 AM
Replies: 6
Views: 2,341
Posted By ikim
Thanks very much for your advice Kmcarr and...

Thanks very much for your advice Kmcarr and bringing up the low complexity issue. That makes a lot of sense, DUST or Seg was on during my initial searches.
I'd run repeatmasker on this sequence...
Forum: De novo discovery 05-21-2013, 03:00 PM
Replies: 6
Views: 2,341
Posted By ikim
Thanks for your suggestion Jeremy. I'll inquire...

Thanks for your suggestion Jeremy. I'll inquire with ENCODE.
I would have thought that non coding rna would have nt annotations at least.
Forum: De novo discovery 05-10-2013, 05:15 PM
Replies: 6
Views: 2,341
Posted By ikim
Unannotated sequence

Hello all,

I have a mystery sequence that I was hoping y'all could help me with.
I've assembled a transcriptome set from both illumina and 454 datasets of the same plant sample. My...
Forum: RNA Sequencing 02-28-2013, 01:53 PM
Replies: 3
Views: 2,507
Posted By ikim
Hi Marc, Thanks very much for your...

Hi Marc,

Thanks very much for your advice. Your pipeline looks very impressive; it runs all of the searches which we use for annotation; i.e. much more indepth than say blast2go. Unfortunately...
Forum: RNA Sequencing 02-27-2013, 12:02 PM
Replies: 3
Views: 2,507
Posted By ikim
GO analysis of RNAseq Assembly

Hi all. I have a plant transcriptome assembled using Trinity that I have annotated with interpro and mapped GO ids to the individual transcripts such that I have a list such as :

comp1_c1_seq1 :...
Forum: De novo discovery 06-23-2011, 03:21 PM
Replies: 82
Views: 47,798
Posted By ikim
My exp is likewise; very small kmer settings for...

My exp is likewise; very small kmer settings for longer reads are far from optimal and take a great deal of resources. My runs are generally 31-61 mer. Memory usage between 8 - 28 GB for our typical...
Forum: De novo discovery 06-01-2011, 10:20 AM
Replies: 82
Views: 47,798
Posted By ikim
From their advanced Guide online "FPKM_all:...

From their advanced Guide online
"FPKM_all: expression value for this transcript computed based on all fragment pairs corresponding to this path.
FPKM_rel: expression value accounting for...
Forum: De novo discovery 05-30-2011, 04:39 PM
Replies: 82
Views: 47,798
Posted By ikim
We have been using Velvet/Oases for denovo...

We have been using Velvet/Oases for denovo transcriptome assembly of several large eukaryotes. I'm running Trinity tests at the moment and it seems to need similar computational resources as our...
Forum: Bioinformatics 12-02-2010, 06:10 PM
Replies: 6
Views: 4,349
Posted By ikim
I would agree in that the multiple kmer approach...

I would agree in that the multiple kmer approach has significantly increased the number of full length contigs in our illumina assemblies, and make much more sense than testing for a single optimal...
Forum: Bioinformatics 12-02-2010, 04:06 PM
Replies: 0
Views: 2,721
Posted By ikim
Unhappy roche 454 adapter filtering

Hi I'm wondering if anyone knows what adapters to filter for with data generated from Rapid library prep, titanium 454 sequencing. There seems to be lots of information about Illumina adapters around...
Forum: Bioinformatics 06-24-2010, 02:12 PM
Replies: 8
Views: 6,694
Posted By ikim
Hello, was wondering how well conserved ribosomal...

Hello, was wondering how well conserved ribosomal RNA, and ribosomal proteins are? How relevant is it to use the Human ribosomal units for matching waterlily datasets for example?
Forum: Bioinformatics 06-11-2010, 03:23 PM
Replies: 0
Views: 879
Posted By ikim
ACE to CAML

Hello guys,
I know this is a shot in the dark, but would anyone know of a way to convert ACE alignment files to the CAML format used in Paracel systems to store assembly information?
Thanks.
Forum: 454 Pyrosequencing 03-08-2010, 11:16 PM
Replies: 29
Views: 13,581
Posted By ikim
Hi, I've come up with a very similar problem...

Hi, I've come up with a very similar problem using TGICL/CAP3 for assembly, but I didn't think it was an issue with memory. Would anyone know if MiraEST can handle a 4 million+ read set? We are...
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