Generate Track 1 And Track 2

[ Main_Page | NGS_data_analysis ]

Create a custom 'GEM-library' Alignability (mappability) track

Credit Card Generator. A valid credit card number has several fields and each of them has a meaning. For the technically inclined, this number complies to the ISO 7812 numbering standard. An contains a six-digit issuer identification number (IIN), an individual account identification number, and a. Track1, track 1, track1 generator, track 1 generator, generate track1, track1 gen, genarator track1, track2gen, generator dumps, track1 generator online. This is the text Generate Track1 from Track2 Dumps The First name. The Last Name. Track2. Track two is a “track” of information that has 40 characters field for information. Track three is a “track” of information that has 107 characters field for alphanumeric information. Credit card contains information on both Track 1 and Track 2. I have Magnetic Swipe Reader, but I can not read the badges I have.

Quick tutorial for beginners new to Logic Pro X on how to create an Output 1-2 track in Logic Pro X. Creating this track in the arrange window allows for ea. Track 2 generator free download. Zint Barcode Generator Encodes data into any of the following: Australia Post barcode, Aztec Code, Aztec Runes, Channel Cod.

(©Derrien et al in 2012, see reference below)

Another tool GenMap^[1] can also produce mappability tracks and is faster than gem

• 2Download reference data
• 3Install and run the GEM library tools
  • 3.2compute Alignability for several K-mer lengths
• 5Conclusion

Results presented here are produced thanks to the method and tools developed by Derrien et al in 2012 ^[2]. We recommend users to fully read this technical paper in order to assimilate subtleties associated with mappability issues and identify limits of short read alignment.

We will create here five kmer alignability track for 16 nuclear chromosomes and the mitochondrial genome of S. cerevisiae strain S288C (sacCer3 obtained from the UCSC FTP repository). This tutorial was mainly built from the developer's web material ^[3].

Any other genome for which the chromosome sequences can be assembles in fasta format and gene annotations are available (optional but important for visualisation) can be processed similarly

Download the yeast reference genome data from the UCSC table repository

• UCSC data can be obtained from their FTP server http://hgdownload.soe.ucsc.edu/goldenPath/sacCer3^[4]
• other files are built from the table browser with interaction in your browser

We use below Kent tools (unix version from ^[5], also available for macOSX^[6]) used by the UCSC team to produce the Genome browser system. Some of these tools should be present on your machine in order to repeat the code below.

download additional SacCer3 annotations

Get the SGD gene table as well as the GC distribution across the whole genome from the UCSC-table (http://genome.ucsc.edu/cgi-bin/hgTables^[7]).

the chromosome names should be identical between the 2bit-fasta and the gene table in order for IGV to display them together

create a 5base step file from the variable step with Kent's hgGcPercent

We can produce the GC% wig file directly from the 2bit genome and name it slightly differently to the downloaded version.

Generate Track 1 And Track 2 Diplomacy

create a bigwig version for rapid visualization

The wigToBigWig command is somehow sensitive to complex fasta headers. If you Fasta sequences have long names including spaces and ':', you should better simplify it and keep only one word like '1' or 'chr1' to avoid problems at this stage

Tools were obtained and installed from : https://sourceforge.net/projects/gemlibrary/files/gem-library/^[8] (the core-2 version was used on the local machine!)

A new version is on the make as of Nov2018 - please read more at https://github.com/smarco/gem3-mapper

The new version Gem3-mapper is not compatible yet with this workflow, you need to use the old version for that and refer to this post https://evodify.com/gem-mappability/

• The current link for the older version is: https://sourceforge.net/projects/gemlibrary/files/gem-library/Binary%20pre-release%203/

there is not yet a version for apple OSX and the source is not available to build locally

create a 'gem' index

compute Alignability for several K-mer lengths

The created index can now be used to compute mapability across the full genome. The alignability / mappability is computed for kmers between 50 and 250 bases by steps of 50 bases and the results are immediately converted to WIG and BigWIG format for IGV visualization.

create for 5 different read sizes

We selected increasing sizes corresponding to read material available on public repositories like SRA and showing the effect of read size on the uniqueness of subsequent short read alignment.

our tracks are based on single-end reads, paired reads are obviously more easily uniquely mapped due to their increased span size that can reach-out from difficult regions

The wigToBigWig command is somehow sensitive to complex fasta headers. If you Fasta sequences have long names including spaces and ':', you should better simplify it and keep only one word like '1' or 'chr1' to avoid problems at this stage

A screen-shot is provided to illustrate the results using IGV and the Broad sacCer3 loaded genome. Other yeast genomes available in IGV include:

Other strains are available from:

• http://genomevolution.org/wiki/index.php/SGRP:_Sanger_Institute_Yeast_Genomes^[10]
• (e.g. Y55) http://genomevolution.org/CoGe/services/JBrowse/service.pl/sequence/9136^[11]

Reads for yeast genome can be obtained from the Sanger institute at:

• http://www.sanger.ac.uk/research/projects/genomeinformatics/sgrp.html^[12]

Generate Track 1 From Track 2 Software

Legend:

• top track represents gene density across the genome for SGD genes
• next 5 tacks show alignability / mappability for increasing kmer length.
• bottom track shows GC% across the genome in 5base bins (scale set between 30 and 50)

Building a custom mappability track is easy and can be done on a laptop for a small genome for which users have the fasta sequence (therefore also for 'contigs' or 'scaffolds' in the case of unfinished genomes). We present here code and results for the current yeast strain that can be adapted for other genomes or strains. The analysis of alignabilty/mappability for paired reads is much more complex and is not produced here, please read the publication for more information.

Generate Track 1 Data From Track 2

Feed back on this page is welcome and can be sent to bits@vib.be

Related reading

A recent paper evaluates the effect of read length on the unicity of mapping (BMC Bioinformatics 2014, 15:2 doi:10.1186/1471-2105-15-2 ^[13])

Download demo files here

1. ↑https://www.biorxiv.org/content/10.1101/611160v1
2. ↑

   Thomas Derrien, Jordi Estellé, Santiago Marco Sola, David G Knowles, Emanuele Raineri, Roderic Guigó, Paolo Ribeca
   Fast computation and applications of genome mappability.
   PLoS One: 2012, 7(1);e30377
   [PubMed:22276185] ##WORLDCAT## [DOI] (I p)

3. ↑http://algorithms.cnag.cat/wiki/The_GEM_library
4. ↑http://hgdownload.soe.ucsc.edu/goldenPath/sacCer3
5. ↑http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64
6. ↑http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386'
7. ↑http://genome.ucsc.edu/cgi-bin/hgTables
8. ↑https://sourceforge.net/projects/gemlibrary/files/gem-library/
9. ↑https://github.com/smarco/gem3-mapper
10. ↑http://genomevolution.org/wiki/index.php/SGRP:_Sanger_Institute_Yeast_Genomes
11. ↑http://genomevolution.org/CoGe/services/JBrowse/service.pl/sequence/9136
12. ↑http://www.sanger.ac.uk/research/projects/genomeinformatics/sgrp.html
13. ↑

    Wentian Li, Jan Freudenberg, Pedro Miramontes
    Diminishing return for increased Mappability with longer sequencing reads: implications of the k-mer distributions in the human genome.
    BMC Bioinformatics: 2014, 15;2
    [PubMed:24386976] ##WORLDCAT## [DOI] (I e)

[ Main_Page | NGS_data_analysis ]