SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 28
Search took 0.01 seconds.
Search: Posts Made By: Marius
Forum: Bioinformatics 10-09-2019, 06:58 AM
Replies: 3
Views: 660
Posted By Marius
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,...
Forum: Bioinformatics 10-06-2019, 07:00 AM
Replies: 0
Views: 423
Posted By Marius
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...
Forum: Bioinformatics 10-04-2019, 07:51 AM
Replies: 1
Views: 523
Posted By Marius
Filtering out individual genotype calls with too HIGH read depth from VCF

I have VCF files generated from GATK's HaplotypeCaller. One file per each of 20 individuals. These VCF files will be combined into a multi-sample gVCF for joint genotyping using GenotypeGVCFs (GATK),...
Forum: Bioinformatics 07-08-2014, 03:11 AM
Replies: 0
Views: 1,181
Posted By Marius
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...
Forum: Bioinformatics 07-04-2014, 07:10 AM
Replies: 4
Views: 1,455
Posted By Marius
I did some more investigating and found the...

I did some more investigating and found the following:

.map-file
1 rs6681049 0 1
1 rs4074137 0 2
1 rs7540009 0 3
1 rs1891905 0 4

1st Column = chromosome
2nd Column = marker ID
Forum: Bioinformatics 07-04-2014, 04:43 AM
Replies: 4
Views: 1,455
Posted By Marius
Great to know! So as it seems I will have to...

Great to know! So as it seems I will have to create 2 input files for PLINK, right (a .ped and a .map file)?

My current SNP data table looks like this:

Ind chrI_1673 chrI_1686 ...
Forum: Bioinformatics 07-04-2014, 02:27 AM
Replies: 4
Views: 1,455
Posted By Marius
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...
Forum: Sample Prep / Library Generation 05-16-2014, 01:49 AM
Replies: 2
Views: 762
Posted By Marius
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...
Forum: Sample Prep / Library Generation 05-13-2014, 10:47 PM
Replies: 2
Views: 762
Posted By Marius
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...
Forum: Sample Prep / Library Generation 05-02-2014, 08:21 AM
Replies: 4
Views: 1,779
Posted By Marius
Good input! Thank's! If there are further...

Good input! Thank's!
If there are further ideas, please let me know!
Forum: Bioinformatics 05-02-2014, 05:53 AM
Replies: 1
Views: 1,597
Posted By Marius
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...
Forum: Sample Prep / Library Generation 05-02-2014, 05:42 AM
Replies: 4
Views: 1,779
Posted By Marius
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...
Forum: Bioinformatics 03-25-2012, 02:05 PM
Replies: 1
Views: 1,231
Posted By Marius
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...
Forum: Ion Torrent 01-12-2012, 04:43 AM
Replies: 4
Views: 6,941
Posted By Marius
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...
Forum: Sample Prep / Library Generation 12-23-2011, 09:32 AM
Replies: 4
Views: 2,925
Posted By Marius
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...
Forum: Sample Prep / Library Generation 12-19-2011, 10:48 PM
Replies: 4
Views: 2,925
Posted By Marius
I haven't loooked at these technologies yet.. ...

I haven't loooked at these technologies yet..

Regarding "multiple": about 120 individuals, 100 kB each, with a good coverage if possible (50 x or so). Preferentially, I would have a single...
Forum: Sample Prep / Library Generation 12-19-2011, 12:31 PM
Replies: 4
Views: 2,925
Posted By Marius
Targeted sequencing of large genomic fagments (100 kb) with NGS

Hi everyone,

I'm looking for a protocol that describes how to sequence in many individuals a specific stretch of DNA of about 100 kb.

My idea is to PCR amplify this genomic sequence by...
Forum: Illumina/Solexa 08-15-2011, 03:05 PM
Replies: 4
Views: 9,340
Posted By Marius
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...
Forum: Illumina/Solexa 08-15-2011, 06:02 AM
Replies: 4
Views: 9,340
Posted By Marius
Sorry, probably beginner question: by overlapping...

Sorry, probably beginner question: by overlapping PCR amplicons you mean just enrich the region of interest with PCR by making several overlapping fragments (how long are those fragments normally?),...
Forum: Illumina/Solexa 08-15-2011, 03:03 AM
Replies: 4
Views: 9,340
Posted By Marius
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,...
Forum: Bioinformatics 05-05-2011, 08:13 AM
Replies: 0
Views: 1,339
Posted By Marius
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...
Forum: General 04-22-2011, 01:10 AM
Replies: 1
Views: 1,780
Posted By Marius
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...
Forum: Bioinformatics 02-17-2011, 11:07 AM
Replies: 3
Views: 3,198
Posted By Marius
Thanks for replying! - I managed do to this so...

Thanks for replying! - I managed do to this so far. But can I somehow get an output with the actual gene names (if available) and their biological function?
Forum: Bioinformatics 02-17-2011, 08:14 AM
Replies: 3
Views: 3,198
Posted By Marius
List all genes belonging to a certain genomic region

Is there a program which I can tell to list me all known genes belonging to a certain genomic region from an existing genome? Or how would you do this?

Thank you for your help.
Forum: Bioinformatics 12-27-2010, 09:38 AM
Replies: 1
Views: 1,621
Posted By Marius
As it seems, what would be best is to do a denovo...

As it seems, what would be best is to do a denovo Assembly (contigs) with all (of all the individuals) my reads (I expect about 40'000 loci), so I'd get about 40'000 contigs, and then use these as a...
Showing results 1 to 25 of 28

 


All times are GMT -8. The time now is 06:43 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO