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Yeah, they'll take a while to get generated.
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Hi... now 24 hours are passed and indexing is still running on my MAc (see previous post of this thread). What can I do now? My processor is dual core... I have to insert an option into the command line to take into account that processor has 2 core?Comment
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24 hours seems excessive. Can you see it still using one of your cores? I don't think the indexing can be run multi-core. What species are you trying to index? Perhaps one of us can just create and post the indices so you can download them.Comment
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simobioinfo is indexing GRCh37/human. If bandwidth is not a problem then you can download the preformatted bundle (sequence, indexes and annotations) from this link: http://support.illumina.com/sequenci...e/igenome.html
@simobioinfo: This is the sort of thing I was trying to warn you about in terms of user experience.
@Devon: If you have indexes for that known to work on a Mac you could post them for simobioinfo.Comment
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I'll give it a whirl on my macbook pro, but it's rather old and low on RAM. Assuming that doesn't work, on Tuesday I'll be back in the office and just use one of our beefier Macs if this isn't resolved by then.Comment
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How much RAM does this Mac have? If you look at my previous post you'll see where I said that if you don't have enough RAM it will take very, very long to build in the index. To build the human genome you probably need 5-6GB but you will have to monitor RAM usage as the index is building to know for sure. And it doesn't matter how many cores you have Bowtie2-build is a single process.Originally posted by simobioinfo View PostComment
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My mac has 4Gb of RAM. I suppose that it could be enough to build index. I don't know how to check ram usage.Originally posted by biocomputer View PostComment
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I was able to build the index on another machine and use it on my macbook pro with 3 gigs of RAM. I really wouldn't recommend doing this on a machine with that little RAM as you end up swapping all the time. Since you have more RAM than my old laptop, hopefully you'll get better performance. I'll post the indices later today and send you a link.Comment
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@simbioinfo: I just sent you a PM with some links to the bowtie2 indices that worked on my Mac. Let me know if they work for you.Comment
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Thank you everybody. I was on vacation. I will try soon indexes you sent meComment
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Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM -
With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.
Introduction
Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...05-22-2026, 06:42 AM
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