Forum: Bioinformatics
08-25-2016, 05:15 AM
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Replies: 3
Views: 1,887
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Forum: Bioinformatics
08-25-2016, 01:04 AM
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Replies: 3
Views: 1,887
VCF specification question
Hi,
I couldn't find this in the VCF specification documents. Is it allowed to have two lines in a VCF with the same variant, identical format & sample columns but different info fields?
edit:...
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Forum: Bioinformatics
08-18-2016, 10:26 PM
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Replies: 0
Views: 1,206
allele order in phased VCF
Hi all,
I know related issues have been discussed before, but I can't find an answer to this specific question:
if you have a phased VCF file, how do the AD fields relate?
would you for...
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Forum: Bioinformatics
04-18-2016, 02:12 AM
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Replies: 0
Views: 2,188
PySAM VCF : add new filter
Hi,
I'm trying to add a new filter to a VCF file after processing using pysam. I can add new format fields to the output header using :
vcf_file = pysam.VariantFile(vcf_path)
new_header =...
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Forum: Sample Prep / Library Generation
04-20-2015, 04:26 AM
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Replies: 1
Views: 1,827
Dual Indexing for NimbleGen SeqCap
Hi all,
For all here performing dual indexed panel resequencing: We just published an adaptation of the seqCap protocol to allow dual indexing and 96 sample multiplexing.
For details, see:
...
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Forum: Metagenomics
08-04-2013, 01:15 AM
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Replies: 1
Views: 1,866
Advies on tool selection
Hi,
I was asked to provide tools in a local galaxy instance to handle the following research question:
Two groups of microbial cultures taken from case and control animals, were 16S sequences...
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Forum: General
05-16-2013, 07:42 AM
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Replies: 0
Views: 1,109
Available Control Trio Exomes
Hi,
I'm looking for publicly available data from some (healthy) trios to use as internal validation runs. AFAIK, the ESP data is not publicly availalbe, and the sample list of 1KG does not list...
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Forum: Bioinformatics
05-15-2013, 08:44 AM
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Replies: 1
Views: 1,192
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Forum: Bioinformatics
08-13-2012, 06:44 AM
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Replies: 8
Views: 90,673
Hi,
I've attached my approach to...
Hi,
I've attached my approach to demultiplexing the MiSeq files. Note that it uses the MiSeq assigned sample idx to name the output files, NOT the barcode. This means you get all reads for the...
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Forum: Illumina/Solexa
08-06-2012, 12:27 AM
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Replies: 1
Views: 2,013
HiSeq 2000 BCL-converter sys. req.
Hi,
We are awaiting the installation of a HiSeq system on our site, and are investigating ICT requirements. We are especially looking for hands-on experience on the following items, as the...
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Forum: Bioinformatics
06-19-2012, 02:21 AM
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Replies: 13
Views: 16,598
To dig up an old thread: I believe the perl...
To dig up an old thread: I believe the perl approach to this function does not fit with the (correct) graphical interpretation that was provided here. As can be seen on the attached plots, reads will...
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Forum: Bioinformatics
02-03-2011, 07:26 AM
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Replies: 4
Views: 2,431
I finally managed to take a look at your...
I finally managed to take a look at your questions. Please retry you query on the website. You will notice that the output has changed for csv results. For each supplied rs_ID, the dbSNP frequencies...
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Forum: Bioinformatics
01-26-2011, 12:30 AM
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Replies: 4
Views: 2,431
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Forum: Bioinformatics
01-17-2011, 05:02 AM
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Replies: 4
Views: 2,431
1KG online data querying
Hi all,
For those interested, we have put online a 1KG data querying website.
Variation can be retrieved based on position, gene name or sequence.
Results are population frequency, total...
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