Forum: Bioinformatics
05-29-2014, 01:15 PM
|
|
Replies: 4
Views: 3,301
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: 2,236
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: 971
|
|
Forum: Illumina/Solexa
12-17-2013, 09:43 AM
|
|
Replies: 2
Views: 3,210
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: 1,967
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: 13,745
|
|
Forum: Academic/Non-Profit Jobs
03-30-2012, 07:33 AM
|
|
Replies: 0
Views: 942
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: 1,363
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: 20,098
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: 1,295
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: 23,191
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: 9,428
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: 3,536
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: 9,371
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: 3,372
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: 16,586
|
|
Forum: Bioinformatics
08-08-2011, 11:23 AM
|
|
Replies: 23
Views: 16,586
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: 5,311
|
|
Forum: Illumina/Solexa
08-03-2011, 09:07 AM
|
|
Replies: 16
Views: 5,311
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: 16,032
|
|
Forum: Illumina/Solexa
08-03-2011, 08:25 AM
|
|
Replies: 12
Views: 16,032
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: 5,311
|
|
Forum: Bioinformatics
07-11-2011, 12:52 PM
|
|
Replies: 23
Views: 16,586
|
|
Forum: Bioinformatics
06-14-2011, 06:11 PM
|
|
Replies: 0
Views: 3,402
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: 8,648
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...
|
