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I am using tophat2 with long index with suffixes .bt21. But it is giving the following error
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Could not find Bowtie 2 index files (.*.bt2)
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As of TopHat v.2.0.11 64-bit bowtie2 indexes were not supported. A new maintenance release is out (v. 2.0.12) but it is likely that long indexes are still not supported. -
Yes, I am using tophat/2.0.12 but still getting that error. Anyway, thanks for your reply.Comment
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try to change "bt2" into "bt2l" in the tophat source file.Comment
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@pengchy: Will this work by changing bt2 to bt2l in source?Originally posted by pengchy View Post
I am using tophat 2.1.0, still have problem of using bt2l. Any solutions so far? I am working on a very genome, so have to use bt2l. Can I align each chromosome separately, and then merge the bam files?Comment
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Yes, I have tested this on tophat-2.0.13.Linux_x86_64/tophat successfully.Originally posted by yifeng View PostComment
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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.
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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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