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Forum: Bioinformatics 03-25-2016, 04:21 PM
Replies: 6
Views: 3,561
Posted By spark
Thanks for the insights & advice - all very...

Thanks for the insights & advice - all very helpful.

We're doing a pilot study comparing sequence reads from a multiplexed PCR of 200 SNP assays with genotypes for the same SNPs generated using an...
Forum: Bioinformatics 03-23-2016, 02:13 PM
Replies: 6
Views: 3,561
Posted By spark
Thanks - I'll look into using that. I've only had...

Thanks - I'll look into using that. I've only had access to the fastq files to date, but I should be able to access the bcl files too.
Forum: Bioinformatics 03-23-2016, 09:51 AM
Replies: 6
Views: 3,561
Posted By spark
demultiplexing dual index Illumina reads with mismatch tolerance

I'm analysing genotyping-by-sequencing data for 2,100 dual-indexed samples and am looking for a fast, mismatch-tolerant demultiplexer.

Libraries for each sample were prepared using a unique...
Forum: Bioinformatics 01-22-2012, 01:32 PM
Replies: 7
Views: 4,199
Posted By spark
Thanks for the suggestion. I've since used the...

Thanks for the suggestion. I've since used the Ensembl variant effect predictor, and it does something very similar to Annovar (which I've already used). The only difference is that the Ensembl...
Forum: Bioinformatics 12-26-2011, 09:01 AM
Replies: 7
Views: 4,199
Posted By spark
SNP function prediction in non-human species

Hello,

I'm trying predict SNP function for a few thousand non-synonymous coding sequence SNPs in cattle. I've looked through the documentation for SIFT and PolyPhen, but can't easily see if they...
Forum: Bioinformatics 03-09-2011, 04:00 AM
Replies: 0
Views: 3,623
Posted By spark
bwa bug? Paired end reads with insert size of 0 flagged as improperly paired

I'm looking at some paired end WGS data from a library with very small insert sizes, meaning that many of the DNA fragments are sequenced fully in both directions.

Reads were aligned to a template...
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