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Forum: Bioinformatics 05-29-2014, 01:15 PM
Replies: 4
Views: 2,119
Posted By greigite
RDP classifier training issues

I am unsuccessfully attempting to retrain the RDP classifier, version 2.7 on the UNITE fungal database. I have tried reformatting and generating a custom tax file with entries like this, following...
Forum: Bioinformatics 02-17-2014, 06:06 PM
Replies: 2
Views: 1,560
Posted By greigite
DESeq2: problem with variance stabilization

I think I am probably missing something obvious here with DESeq2. I used to use DESeq frequently to normalize count data but somehow cannot get the same process to work in DESeq2. I am able to create...
Forum: Bioinformatics 01-17-2014, 10:55 AM
Replies: 1
Views: 555
Posted By greigite
any instrument with onboard 16s analysis capability?

Does anyone know if any of the benchtop instruments from Illumina or Ion have the capacity to do on-board or cloud based analysis of 16s rRNA amplicon sequences? Something like mapping sequences to...
Forum: Illumina/Solexa 12-17-2013, 09:43 AM
Replies: 2
Views: 2,340
Posted By greigite
Dereplication tools needed

It's been a while since I got my hands on shotgun Illumina metagenomic data. I've found that it's quite important to dereplicate before doing any downstream analysis to avoid problems with assembly...
Forum: Bioinformatics 07-31-2012, 11:31 AM
Replies: 0
Views: 1,271
Posted By greigite
removing duplicate PE reads from unmappable data

This topic has been discussed a fair bit on seqanswers but I haven't found the answer to this exact question, so am throwing it out there again. I have some 100 bp PE metagenomic data sets from...
Forum: Bioinformatics 03-30-2012, 11:57 AM
Replies: 21
Views: 10,747
Posted By greigite
DESeq provides a test data set "pasilla,"...

DESeq provides a test data set "pasilla," described in the vignette. Not sure if that's what you are looking for.
Forum: Academic/Non-Profit Jobs 03-30-2012, 07:33 AM
Replies: 0
Views: 649
Posted By greigite
Repost: Bioinformatician, MBL

The position of Scientific Informatics Analyst at the MBL in Woods Hole remains open and we welcome additional applications at https://mbl.simplehire.com/postings/2167/.


Position Summary: The...
Forum: Academic/Non-Profit Jobs 01-26-2012, 09:21 AM
Replies: 0
Views: 967
Posted By greigite
Scientific Informatics Analyst, MBL

Please apply online through MBL SimpleHire (https://mbl.simplehire.com/postings/2167). Note, this is an initial one-year position with the possibility of extension. The job is located at the Marine...
Forum: Illumina/Solexa 11-18-2011, 02:04 PM
Replies: 38
Views: 15,715
Posted By greigite
For what it's worth we sequenced two lanes on a...

For what it's worth we sequenced two lanes on a HiSeq (v2 flow cell) containing 11 7 bp inline barcodes with a spike-in of 5% phiX. Despite the low diversity visible in fastqc plots for the first 7...
Forum: Illumina/Solexa 10-13-2011, 01:20 PM
Replies: 0
Views: 850
Posted By greigite
stored diluted libraries- can they be re-run?

Does anyone have experience with long-term storage of libraries diluted into the flow cell loading buffer (so at ~8-10 pM)? We have quite a bit of this dilution left over from a run ~5 months ago and...
Forum: Illumina/Solexa 10-11-2011, 05:03 PM
Replies: 10
Views: 18,187
Posted By greigite
dual indices?

Does anyone have experience with Illumina's new "dual indexing" method in the Nextera kits? I guess this is their new multiplexing strategy, with different indices on adapter 1 and adapter 2....
Forum: Vendor Forum 10-05-2011, 02:56 PM
Replies: 36
Views: 7,075
Posted By greigite
Interesting thread. I thought I'd share our...

Interesting thread. I thought I'd share our practical experience with rRNA depletion from microbial RNA extracted from soils. We compared epicentre's previous enzymatic-based kit (mRNA only...
Forum: RNA Sequencing 10-05-2011, 02:41 PM
Replies: 8
Views: 2,469
Posted By greigite
There seem to be two strategies for a pooled...

There seem to be two strategies for a pooled assembly:
1) pool all transcriptome reads from all varieties, then assemble
2) pool only consensus contig sequences from your variety-specific...
Forum: Sample Prep / Library Generation 09-27-2011, 05:57 AM
Replies: 22
Views: 6,767
Posted By greigite
The specs for the AIR kits say they can be used...

The specs for the AIR kits say they can be used with as little as 50 ng input material. Has anyone tried these kits using less than that? Any successes or failures? We have samples with only ~10 ng...
Forum: Bioinformatics 08-09-2011, 11:06 AM
Replies: 2
Views: 2,534
Posted By greigite
I don't know a tool that combines both, but a...

I don't know a tool that combines both, but a work-around pipeline might be to:
1) split read 1 file with fastx_barcode_splitter
2) construct lists of reads from each library
3) extract those...
Forum: Bioinformatics 08-08-2011, 02:43 PM
Replies: 23
Views: 11,546
Posted By greigite
Thanks for the responses, sounds like I might be...

Thanks for the responses, sounds like I might be doing something else wrong with cdbfasta that's causing it not to work properly.
Forum: Bioinformatics 08-08-2011, 11:23 AM
Replies: 23
Views: 11,546
Posted By greigite
cdbfasta

One issue I've noticed with using cdbfasta -Q to index fastq files is that it uses the "@" character as a record delimiter. That works if the qual scores use phred+64 encoding but not if they use...
Forum: Illumina/Solexa 08-03-2011, 10:04 AM
Replies: 16
Views: 3,955
Posted By greigite
Great suggestion. Unfortunately, my libraries are...

Great suggestion. Unfortunately, my libraries are metagenomes- so no reference is available. I hope someone else will be able to do this analysis and post the results!
Forum: Illumina/Solexa 08-03-2011, 09:07 AM
Replies: 16
Views: 3,955
Posted By greigite
no periodicity in xenopus data

Update on my last post: I do not see the 3 bp periodicity in someone else's Xenopus sequence capture libraries sequenced in another lane of the same flow cell as my microbial libraries, except...
Forum: Illumina/Solexa 08-03-2011, 08:58 AM
Replies: 12
Views: 14,618
Posted By greigite
My concern is whether those q30-32 scores for the...

My concern is whether those q30-32 scores for the first 3 bases have anything to do with reality. Another user here has some data from amplicon sequencing that suggests they do not (variation from...
Forum: Illumina/Solexa 08-03-2011, 08:25 AM
Replies: 12
Views: 14,618
Posted By greigite
We are seeing the same thing with exactly the...

We are seeing the same thing with exactly the same step pattern of quality. I'm not sure how to handle this downstream since it essentially means that the quality scores in the first three bases, and...
Forum: Illumina/Solexa 08-02-2011, 09:14 PM
Replies: 16
Views: 3,955
Posted By greigite
I read this thread with great interest because I...

I read this thread with great interest because I have just discovered the same 3 bp periodicity artifact in some of my recent data, though it's not as strong as the OP's. I have microbial metagenomic...
Forum: Bioinformatics 07-11-2011, 12:52 PM
Replies: 23
Views: 11,546
Posted By greigite
I tried this script but it doesn't seem to play...

I tried this script but it doesn't seem to play nice with fastq files that don't contain the sequence name after the "+" before the quality score line (which is optional):

Fastq file:

@seq1...
Forum: Bioinformatics 06-14-2011, 06:11 PM
Replies: 0
Views: 2,607
Posted By greigite
time series analysis of count data?

It hasn't been that long since Simon's post below in this thread: http://seqanswers.com/forums/showthread.php?t=5793 but is there anything new out there in terms of applying microarray time series...
Forum: Metagenomics 06-14-2011, 05:50 PM
Replies: 7
Views: 6,395
Posted By greigite
We use a similar protocol to the PLoS One paper...

We use a similar protocol to the PLoS One paper in that we create metagenomic libraries with narrow insert size distributions, sequence overlapping 100 bp PE reads, and assemble computationally. We...
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