MacVector and macOS Mojave

By Chris | Published: September 25, 2018

Apple released macOS Mojave today (Tuesday 25th September).

Over the past few months we have performed preliminary testing with MacVector 16.0.9 on various development releases of macOS Mojave through its development cycle and all appears to be well.

So whereas we cannot state MacVector is compatible until it is officially released, we can say that we think all is OK.

Incidentally over the past few releases of MacVector we have made significant effort to future proof MacVector for upcoming releases of macOS.

Please do note that MacVector 16.0.9 will not support Dark Mode. However, it is planned for the next release, MacVector 17 (out later this year).

For older versions of MacVector you can check compatibility on our website. The results for macOS Mojave are not yet published, but it is likely that they will follow the ones for macOS High Sierra 10.13.4.

Please note that we do generally recommend that you do not upgrade to a new macOS release until at least a few weeks after a release.

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Free MacVector Teaching licenses

By Chris | Published: September 11, 2018

Did you know that MacVector, Inc. offers FREE licenses for teaching purposes?

If you are in the process of either preparing your lab for the upcoming year, or preparing for the courses you need to teach then don’t forgot that MacVector makes a great teaching tool. We offer free teaching licenses for anyone with an active, up-to-date license. All we need for your teaching license is the course name and number, start and stop date of the course, and the number of seats needed. We also have many great resource materials that will help you or your students learn MacVector.

Send my free teaching license →
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NOW CANCELLED MacVector are at the NIH Research Festival

By Chris | Published: September 7, 2018

NIH Research Festival Tent show September 13-14, 2018

Due to the forecast storm the Tent Show has been postponed. As soon as we know the rescheduled date we’ll update.

We’re at the NIH Research Festival this week. Please drop by our booth on Thursday or Friday, when the big, white exhibitors tent is open. We’re on Booth #520 on parking lot 10H.

We enjoy the tent show and look forward to meeting NIH MacVector users both new and old, and anybody who is interested in learning to use the easiest to use sequence analysis application for the Mac. We’re happy to just have a chat, but we’ll also be able to give you a preview of our next release, MacVector 17.0, which will be out soon (automatic Gibson assembly, Compare Genomes, and much more!). We’ll have some goodies too – our popular mousepads with the IUPAC Genetic Code as well as some Pop sockets for your cell phone.

The exhibit hours are:

  • Thurs. Sept 13 from 9:30 to 15:30
  • Fri. Sept 14 from 9:30 to 14:30

    • Don’t forget that the NIH host a Picnic. There will be food from several restaurants being sold at a discount for both researchers and exhibitors.

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    MacVector and future releases of macOS

    By Chris | Published: August 1, 2018

    The next OS release for the Mac will arrive later this year. MacOS Mojave is a significant OS upgrade and includes a lot of new features, especially when compared with the differences between OS X El Capitan, macOS Sierra and macOS High Sierra.

    Our developers have been hard at work ensuring that when macOS Mojave is released, MacVector 16 and the following release (MacVector 17) will be fully compatible.

    As usual for older versions you can check compatibility on our website. The results for macOS Mojave are not yet published, but it is likely that they will follow the ones for macOS High Sierra 10.13.4.

    For recent older versions it is likely that they will work fine. Over the past few version we have been striving to future proof MacVector for new versions of macOS.

    However, for older versions of MacVector there will be issues. Apple do make significant changes between releases. One issue that you will see with MacVector 13.5 and earlier versions is regular dialogs stating that this version of MacVector will not work with the next release of macOS.

    A more subtle version of this dialog started appearing with the release of macOS High Sierra 10.13.4, when Apple added warnings to all 32 bit applications.

    Here at MacVector we always strive to stay ahead of the game. When Apple recommended (many years ago) that all applications should be 64 bit, we immediately started working to move MacVector to be fully 64 bit resulting in the release of MacVector 14 in 2015.

    Please do note that whereas our developers do develop and run MacVector on Apple’s public and developer betas of macOS, we really do not recommend that users run MacVector for any real workflows on beta releases. There may be unexpected issues that you may encounter.

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    RNASeq Expression Analysis with MacVector and Assembler

    By Chris | Published: June 25, 2018

    If you have the Assembler module, MacVector can align millions of NGS reads from RNASeq experiments against large genomes and generate a coverage table displaying the relative expression levels of every gene in a genome. The key to this functionality is that you must have a reference genome with genes annotated as CDS or gene features – then you can use Bowtie to rapidly assemble reads from fastq files against the genome and generate a report listing the coverage for each feature. The steps to do this are:

  • Use File | New | Assembly Project to create a new project.
  • Click on the Add Ref toolbar button to add a suitable annotated reference genome.
  • Click on the Add Reads toolbar item to add your RNASeq reads.
  • Click on the Bowtie toolbar button to assemble the reads against the reference genome.
  • Double-click on the resulting reference contig item and switch to the Coverage tab.

    • You will get a display similar to this.

    NewImage

    This lists each CDS and gene feature, along with the number of reads that aligned to each feature and the Reads Per Kilobase of transcript per Million mapped reads (RPKM) and Transcripts Per Kilobase Million (TPM) values that can be used to compare expression between genes and runs.

    There is an RNASeq Expression Analysis Tutorial available that describes this functionality in more detail. If you are running MacVector 16.0.4 or later you will find this in the /Applications/MacVector/Documentation/ folder. Otherwise you can download the tutorial and sample dataset. Although this is a small dataset designed for rapid analysis, you can use this approach to align 50 million+ reads against the entire human transcriptome on a modest (16 GB RAM) MacBook Pro.

    Not sure if you have Assembler? Choose MacVector | About MacVector. If the screen that appears says “MacVector with Assembler, Pro Edition” then you have it. If not, you can sign up for a fully functional 21 day trial version.

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    How to split large fastq files for more manageable assemblies

    By Chris | Published: June 25, 2018

    We’ve previously discussed how important it can be to make sure you are using the appropriate number of fastq reads from an NGS experiment to ensure you obtain the results you are looking for. Using too many reads can confuse algorithms with the massive coverage increasing mis-assemblies due to background errors in the reads. In addition, large numbers of reads can significantly impact CPU performance, memory usage, and even disk usage. At MacVector we have coded a simple utility that will split large fastq files into smaller chunks. It’s completely free to download and should work on all versions of macOS/ Mac OS X.

    Download the SplitFastqFile utility

    You run it by simply dropping fastq files onto the application and following the prompts. When complete, you’ll see the split files in a folder, with naming similar to this.

    (Read more….)

    NewImage

    Not sure if you have Assembler? Choose MacVector | About MacVector. If the screen that appears says “MacVector with Assembler, Pro Edition” then you have it. If not, you can sign up for a fully functional 21 day trial version.

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    Balancing Velvet KMER and coverage

    By Chris | Published: June 12, 2018

    The Velvet assembly algorithm in MacVector is blazingly fast and generates excellent assemblies. However, you do have to be careful when assembling NGS data to be sure that the parameters you submit are appropriate for the data you are assembling in order to get optimal results. By far the most important parameter is the KMER value. If you are not getting good assemblies, this is the parameter you should change. Below are the results of varying the KMER value for an NGS assembly of a circular 8,859 bp plasmid using data acquired from an Illumina HiSeq machine. In this case, the data consisted of a pair of fastq files with a read length of 75 nt. The original files each contained 1,370,000 paired end reads. The table below shows the longest contig that resulted from using varying numbers of input reads, versus varying the KMER parameter in Velvet.

    MacVector has a feature in the contig editor that simplifies circularization of contigs with overlapping direct repeats at the ends. All the contigs in black could be circularized to generate a 8,859 bp plasmid. Those in red were not full length, or could not be circularized.

    • First, note that Velvet (like most assemblers) does not like a massive over-abundance of coverage. If you submit too many reads, it confuses the algorithm and you have to be very careful with your choice of KMER to get a good assembly.

    • Second, note that the more reads you submit, the higher the KMER needs to be to generate a complete contig.

    The take home lesson from this is that in general, you should tune the amount of data in your NGS set to be between 100x and 1,000x coverage as that gives the most flexibility in your choice of KMER. You should start with a KMER that is ~70% of the average length of your reads (it has to be odd, so 51 in this case), then vary the KMER to see what impact that has. This holds true for bacterial genome assemblies as well as simple plasmids like this. Next week we will discuss a tool to help you break up large NGS data files into smaller segments to facilitate this analysis.

    Not sure if you have Assembler? Choose MacVector | About MacVector. If the screen that appears says “MacVector with Assembler, Pro Edition” then you have it. If not, you can sign up for a fully functional 21 day trial version.

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    Use a right-click in the Editor tab to see if your contig can be circularized

    By Chris | Published: June 6, 2018

    MacVector 16 incorporates no less than THREE different de novo assemblers, phrap, velvet and SPAdes. While all are great assemblers, with each having their own specific advantages, none of them will generate a circular sequence from input reads. However, MacVector 16 also includes a new feature to help you with this. If you are assembling reads representing plasmid sequences, or if you are closing gaps in a circular genome, you can find out if a contig can be circularized by double-clicking on it in the Assembly Project and then right-clicking* in the Contig Editor to bring up a context-sensitive menu.

    NewImage

    The algorithm looks for a perfect overlap between the ends of at least 20 bases. If no overlap exists, the menu item is greyed out and reads “Cannot Circularize Consensus”. Otherwise it indicates the length of the overlap. If you select the menu item, a new sequence window opens containing the circularized consensus of the contig, with all gaps removed.

    *To right click with a trackpad hold down [CTRL] and click once or tap with two fingers. MacVector has many “right click” menus with extra functionality.

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    Getting Started with MacVector

    By Chris | Published: June 4, 2018

    Any molecular biologist should be able to start getting useful results within an hour of starting to use MacVector by just exploring the toolbar and menus. Everything is logically named to be obvious. However, there’s still a lot of functionality that a user will never know exists. That is unless you read the manual or the help pages and we all know nobody does that any more!
    This blog post shows all the different resources we have available to help you get the most of MacVector.

    But before you read the following resources, please always remember that the MacVector Support Team is only ever an email away. We will always reply back within a working day, generally much quicker than that! There is no such thing as a stupid or trivial question and we genuinely enjoy hearing from users. Even if you just want to tell us about your work, and ask how MacVector can help!

    Before you proceed watch this video on how to directly download a sequence into MacVector from the Entrez database. It’s always better to learn with your own sequences!

    Getting Started guide

    The first document that any user should turn to is Getting Started with MacVector. This document is geared for both new users and those who already use MacVector and introduces you to the new functions and features in recent versions.

    Tutorials

    In the documentation folder right in MacVector you will find some PDF tutorials. All these tutorials work using sequence files that you will find directly in the “Tutorial Files” section of the MacVector application folder.

    Up to date tutorials are always available on our website

    How Do I? Menu

    New to MacVector 17 is a menu with access to short videos and step by step guides to many common workflows.

    Screenshot 2019 07 02 at 12 52 38

    Every tool’s dialog also has a direct link to a video/guide on how to use that tool.

    MacVector Help

    For specific and up to date information turn to the MacVector Help directly within the MacVector Application itself.

    Weekly tips email newsletter

    We have a short weekly email with tips on using MacVector. Most of the tips are answers to questions that have recently been asked by users. We think that if someone has a question about it, then others probably do too! We will never forward your information on to a third party and you are able to easily unsubscribe from these emails.
    Every email is meant to be read in a few minutes or quickly skipped if it is not relevant. They rarely have more than three short paragraphs.
    Here are some past posts.

    101 tips

    These blog posts show short tips into MacVector’s functionality.

    Screencasts

    Sometimes a video is more instructional than text. There are short video tips on using MacVectoron our blog and our YouTube channel
    These cover subjects as diverse as adding primers to the Primer database, or aligning large sequencing reads datasets against a genome. Each one is less than 2 minutes and generally shorter than that!
    The latest screencasts include showing Missing Features on unannotated sequences, searching for sequences in the Entrez database checking the orientation of a ligated insert using MacVector’s Restriction Digest and Agarose Gel tools.

    Workshops

    We will come and run real live workshops for your research group or institute. Email MacVector Support to find out about workshops in your area.

    Documentation

    The documentation folder in the MacVector application folder (Finder Window> Applications > MacVector > Documentation); as well as our website contains many excellent resources:

    Manuals

    • The MacVector 16.0 Workshop Manual is geared for those who already use MacVector and introduces you to the new functions and features in MV 10.0 through 16.0. It is still useful if you are not very familiar with any version of MacVector.
    • The latest version of the full MacVector User Guide, MV 12.6 (July, 2012) is available in PDF format. This is the most recent edition of the User Guide. We update the User Guide every couple of years.

    What’s New in MacVector

    Here’s a list of all new features over the many versions.

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    The MacVector Team are at ASM Microbe 2018 in Atlanta this week.

    By Chris | Published: June 4, 2018

    We’re at ASM Microbe 2018 in Atlanta from Friday until Sunday (8–10th June).

    The exhibit hall hours are again different from the last two years.

  • Friday, June 8th – 10:30 AM – 5:00 PM
  • Sat. June 9th – 10:30 AM – 5:00 PM
  • Sunday, June 10th – 10:00 AM – 4:00 PM

    • We’re on booth 1410.

    Please do drop by. We’ll be showing our latest release, MacVector 16, and previews of our upcoming release MacVector 17.

    If you’ve never used MacVector before, or you are a power user, then please drop by and say hello. We guarantee we can teach you something new. If not, then hopefully you’ll be able to teach us something new.! So it’s a win:win for all.

    See you in Atlanta!

    Kevin and Chris in Boston ASM2016

    The Twitter hashtag looks to be #ASMMICROBE2018.

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