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Forum: De novo discovery 01-21-2017, 12:19 PM
Replies: 5
Views: 6,236
Posted By NYGen
Hey GAFA, I would look into estimating repeat...

Hey GAFA, I would look into estimating repeat content, which you can do with Repeat Explorer (there was at my last check a Galaxy server specifically for doing this analysis quickly in a GUI). My...
Forum: Bioinformatics 08-28-2015, 11:34 AM
Replies: 3
Views: 1,226
Posted By NYGen
Thanks a million for recommending DELTA-BLAST;...

Thanks a million for recommending DELTA-BLAST; that was absolutely what I needed. Also, legitimately cool paper. Cheers
Forum: Bioinformatics 08-27-2015, 10:59 AM
Replies: 3
Views: 1,226
Posted By NYGen
I've been reading NCBI's tutorial on PSI-BLAST...

I've been reading NCBI's tutorial on PSI-BLAST (http://www.ncbi.nlm.nih.gov/books/NBK2590/) and it's looking like the tool I should use. Other recommendations are of course welcome
Forum: Bioinformatics 08-27-2015, 09:49 AM
Replies: 3
Views: 1,226
Posted By NYGen
Looking for the right tool for very-distantly-related similarity search

Hello Seqanswers,

I need some help in deciding which tool (preferably web-based) is best for searching for very-distantly related homolog genes. I have a set of 100 human genes (all with...
Forum: Illumina/Solexa 08-14-2015, 09:04 PM
Replies: 5
Views: 8,704
Posted By NYGen
Wow, this was extremely helpful. Thanks very much...

Wow, this was extremely helpful. Thanks very much for the explanation HESmith and Brian, and also MU Core for the technote which I've saved for future reference. Cheers
Forum: Illumina/Solexa 08-12-2015, 09:20 PM
Replies: 5
Views: 8,704
Posted By NYGen
WHY are the first few bases of Illumina HiSeq reads of lower quality?

Hello Seqanswers,

I'm trying to learn: Why are the first few bases of Illumina HiSeq reads of lower quality? This general impact of this question makes it feel like it has been asked numerous...
Forum: Bioinformatics 07-11-2015, 06:39 PM
Replies: 0
Views: 1,399
Posted By NYGen
MAKER prerequisites and dependencies

Hello all,

I'm a biologist trying to be a bioinformatician, and I'm doing a local installation of MAKER on my own, which requires a bunch of perl modules (no problem) and external programs...
Forum: De novo discovery 06-09-2015, 02:35 PM
Replies: 5
Views: 6,236
Posted By NYGen
@pmiguel - I doubt that the FCM analysis is off,...

@pmiguel - I doubt that the FCM analysis is off, as we did 3 replicates and they were consistent around the value from above. I hear you, though, about the possibility of standards being off, so I'm...
Forum: De novo discovery 06-05-2015, 01:07 PM
Replies: 0
Views: 2,192
Posted By NYGen
Why is predicted best k for de novo assembly so different from actual best k?

Greetings everyone,

Iím doing my first genome assembly for a non-model plant species, and I need some insight about best kmer lengths for DBG-based assembly. My NGS data is a full lane of Illumina...
Forum: De novo discovery 06-05-2015, 01:02 PM
Replies: 5
Views: 6,236
Posted By NYGen
Large discrepancy between de novo assembly versus actual biological genome size

Hello everyone,

Iím in the midst of assembling a eukaryotic genome for the first time, working in a non-model plant species, and I could use some insight: my data consists of reads from a full...
Forum: Sample Prep / Library Generation 06-03-2015, 11:57 AM
Replies: 2
Views: 2,149
Posted By NYGen
Perfect, thanks very much for the explanation....

Perfect, thanks very much for the explanation. Cheers!
Forum: De novo discovery 06-03-2015, 11:40 AM
Replies: 0
Views: 1,724
Posted By NYGen
Considering paradoxical assemblies and a question about repeat content estimation

Edit: to allow my question to be more useful to future researchers with similar questions, I've split my long, multi-paragraph series of questions into a pair of shorter questions. These posts can be...
Forum: Sample Prep / Library Generation 06-02-2015, 05:15 PM
Replies: 2
Views: 2,149
Posted By NYGen
After 1st-strand cDNA synthesis for RNAseq, is it safe to wait a day for 2nd?

Greetings All,

It's my first time doing library prep for RNAseq on a eukaryotic organism, and unfortunately I failed to order 2nd strand cDNA synthesis mix before the end of business today, so...
Forum: De novo discovery 04-14-2015, 03:37 PM
Replies: 1
Views: 1,511
Posted By NYGen
Remove subset of good reads to improve genome assembly

Hello seqanswers,

I'm de novo assembling a diploid genome (haploid genome = 200Mb) with reads from Illumina Hiseq V4 2x125 (high-output) from a full lane of one library only with an insert size =...
Forum: Bioinformatics 01-24-2015, 01:19 PM
Replies: 2
Views: 3,320
Posted By NYGen
I also have this question - if anyone has insight...

I also have this question - if anyone has insight on this, could you offer some?

Thanks very much!
Forum: Bioinformatics 01-11-2015, 07:16 PM
Replies: 1
Views: 1,471
Posted By NYGen
Genome to assemble- need hardware help!

Hey Seqanswers- I'm in a bind,

I'm soon going to be in receipt of Illumina Hi-seq PE genomic reads for a non-model plant with genome about 400Mb. I'm OK re software for de novo assembly, but my...
Forum: Illumina/Solexa 08-22-2014, 11:37 AM
Replies: 3
Views: 2,165
Posted By NYGen
Wow. Cannot believe that none of my searches...

Wow. Cannot believe that none of my searches returned either of these. 1000 thanks GenoMax, you really just turned my day around.
Forum: Illumina/Solexa 08-22-2014, 11:07 AM
Replies: 3
Views: 2,165
Posted By NYGen
Shopping for HiSeq run

Hello all- I'm trying to do some research to find the best deal to get whole genome sequencing done with HiSeq paired-end 2x100bp. I've already read over this list...
Forum: Introductions 08-22-2014, 06:07 AM
Replies: 2
Views: 1,192
Posted By NYGen
Thanks

Thanks very much for the advice, I'm about to start doing just that.
Forum: Introductions 08-21-2014, 10:39 AM
Replies: 2
Views: 1,192
Posted By NYGen
Direction! I could use some!

Hello SEQanswers!

Where should a guy go to get practice for learning de novo genome assembly?

Thanks for any help!
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