Forum: Bioinformatics
11-03-2020, 11:45 AM
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Replies: 0
Views: 619
Constrained ordination with SNP data
I have a genome-wide SNP dataset from RADseq containing 100 individuals from 4 groups. I converted the data so that it's in the form of a matrix (columns are SNPs, rows are individuals).
I'd like to...
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Forum: Bioinformatics
10-09-2019, 06:58 AM
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Replies: 3
Views: 1,313
Remove a part of a filename in a Bash loop
I have many files named like this:
lib01.GFBAG_UHAU.fastq.sam.bam
lib02.ABABAB_ZU.fastq.sam.bam
lib03.ZGAZG_IAUDH.fastq.sam.bam
Many parts of the filenames are thus variable in length,...
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Forum: Bioinformatics
10-06-2019, 07:00 AM
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Replies: 0
Views: 935
Problem using BASH to pipe Piccard command
I'm new to Bash, but would like to use it.
I would like to pipe two Picard (GATK pipeline) commands using Bash. Each of these commands works fine when they are run as individual Bash scripts (see...
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Forum: Bioinformatics
10-04-2019, 07:51 AM
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Replies: 1
Views: 1,656
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Forum: Bioinformatics
07-08-2014, 03:11 AM
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Replies: 0
Views: 1,372
Haplotype Block size estimateion using PLINK
I would like to use PLINK to infer haplotype block size estimations. The manual tells me the following: "Note that only individuals with a non-missing phenotype are included in this analysis." In...
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Forum: Bioinformatics
07-04-2014, 07:10 AM
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Replies: 4
Views: 1,742
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Forum: Bioinformatics
07-04-2014, 04:43 AM
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Replies: 4
Views: 1,742
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Forum: Bioinformatics
07-04-2014, 02:27 AM
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Replies: 4
Views: 1,742
LD along genome, R or PLINK?
Hi everyone!
I have a dataset of SNPs along chromosomes (physical positions are available) of several individuals from natural populations. I'm now interested in calculating LD along these...
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Forum: Sample Prep / Library Generation
05-16-2014, 01:49 AM
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Replies: 2
Views: 890
I'm less interested in such genes because of...
I'm less interested in such genes because of technical reasons, but more in terms of evolution. So which genes/gene classes are generally thought to be rather conserved through evolution, and which...
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Forum: Sample Prep / Library Generation
05-13-2014, 10:47 PM
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Replies: 2
Views: 890
polymorphic and conserved genes
Hi everyone!
I'm interested in finding genes which are generally considered to be a) highly polymorphic (possibly driven by balancing selection), and b) conserved ('stable'). I'm looking for genes...
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Forum: Sample Prep / Library Generation
05-02-2014, 08:21 AM
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Replies: 4
Views: 1,978
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Forum: Bioinformatics
05-02-2014, 05:53 AM
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Replies: 1
Views: 1,804
fastPHASE to Haploview
Hi everyone!
Is anyone familiar with Haploview? If so, could you tell me whether it is possible to input fastPHASE output file formats into Haploview?
If not, I have my information in the...
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Forum: Sample Prep / Library Generation
05-02-2014, 05:42 AM
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Replies: 4
Views: 1,978
Balance many PCR products for pooling
Hi everyone!
I'm currently doing a project in which I PCR amplify (long-range PCR) 20 genomic fragments (each of 5-10 kb in length) in 50 individuals. The aim is then to pool fragments of the same...
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Forum: Bioinformatics
03-25-2012, 02:05 PM
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Replies: 1
Views: 1,389
Inferring (visualizing) haplotypes
Hi everyone,
I have about 300 SNPs from about 200 individuals for a region covering 6mb of a genomic region (reference available). All these individuals are wild caught, so there is no knowlege...
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Forum: Ion Torrent
01-12-2012, 04:43 AM
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Replies: 4
Views: 7,777
Software to process IonTorrent data
Does anyone of you have experience with different softwares available for processing Ion Torrent data? Or could you recommend a certain software?
I found these four also suggested on the Ion...
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Forum: Sample Prep / Library Generation
12-23-2011, 09:32 AM
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Replies: 4
Views: 3,159
Thank you!!! I actually found this kit by...
Thank you!!! I actually found this kit by Illumina: TruSeq Custom Amplicon (TSCA).
Does anyone have experience with it? Is it well suited to e.g. sequence 4 different 96kb genomic fragments in...
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Forum: Sample Prep / Library Generation
12-19-2011, 10:48 PM
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Replies: 4
Views: 3,159
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Forum: Sample Prep / Library Generation
12-19-2011, 12:31 PM
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Replies: 4
Views: 3,159
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Forum: Illumina/Solexa
08-15-2011, 03:05 PM
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Replies: 4
Views: 9,533
Thanks a lot for your answers. - How about...
Thanks a lot for your answers. - How about single-end, would this even be good enough quality? And how about 76 cycles single-end? Since I have some reads left (about 15 Mio) within a 76-single end...
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Forum: Illumina/Solexa
08-15-2011, 06:02 AM
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Replies: 4
Views: 9,533
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Forum: Illumina/Solexa
08-15-2011, 03:03 AM
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Replies: 4
Views: 9,533
Illumina to sequence region of 50 kB
Hi there,
is it possible to somehow entirely sequence a region of 50 kB (reference genome available) from a specific chromosome of one individual with Illumina sequencing (100 cycle runs)? If so,...
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Forum: Bioinformatics
05-05-2011, 08:13 AM
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Replies: 0
Views: 1,587
Heat map
On Ensembl, one can look at gene densities along the chromosome of organisms. However, one cannot get this data, which is crucial to create a heat map.
I'd like to create such a gene density map...
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Forum: General
04-22-2011, 01:10 AM
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Replies: 1
Views: 2,012
Recombination mapping
I have some conceptual issues concerning the construction of a "recombination map": If I have many F2 genotyped for genome-wide SNP markers as well as their grandparents (parental generation), how...
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Forum: Bioinformatics
02-17-2011, 11:07 AM
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Replies: 3
Views: 3,543
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Forum: Bioinformatics
02-17-2011, 08:14 AM
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Replies: 3
Views: 3,543
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