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We're running and mapping human samples on our new(ish) HiSeq2000 and we're seeing some low mapping rates out of ELAND. Even if you don't run ELAND, I'd be interested in hearing what other HiSeq users' mapping rates look like with Bowtie/BWA/whatever.
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I have used bowtie to map illumina RNA-seqs to the original genome. The mapping rate is 6.98% without considering repeat mapping. The true rate is even lower. -
6% is kind of surprisingly low. We're seeing 20% on our transcriptome runs with Bowtie, but I suspect that may have something to do with the library construction and how the paired reads may overlap (which Bowtie can not deal with, minimum insert size is 0).Comment
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I am currently not using PE. All available is a single fasta file of reads. I have tested two totally different bacteria species. Both of them are of this level, i.e, mapping rate is pretty low. I do not know the reason. Any suggestions?Originally posted by Lee Sam View PostComment
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I realize the OP asked about the HiSeq. We don't have a HiSeq, but I wouldn't expect the results to be very different from the GAIIx since they use the same chemistry so I'll throw this out there for comparison.
We recently sequenced a maize transcriptome with 101bp single end reads. We truncated to 76 bp and used tophat, which uses bowtie, and we were able to map 66% of the reads.
I think something is wrong if you are only mapping 6%. Was the library ribo-depleted or polyA? Was the library checked on a bioanalyzer to see if primer-dimers were present and to assess how much rRNA was present in the sample? We have had user prepared libraries that have had as much as 80% rRNA present in the final library.Comment
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We have good mapping rates with HiSeq RNA-seq on human samples, >70% and up to ~80% with bwa or TopHat. (PE 2x100)Comment
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Is this mapping to the genome or the transcriptome (coding exons)?
Also, if your RNA has mycoplasma contamination (from cell culture) you will get much lower mapping rates.Comment
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I am sorry. I made a mistake calculating the statistics. The mapping rate is 77.45%. However, most of the mapped sequences are duplicately mapped. I am not doing the sequencing part of research. I am doing the annotation part. So I am not clear of the details of the sequencing.Originally posted by kopi-o View Post
best wishes!Comment
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I am mapping the sequences to the original genome. I am not clear of the environment. I am doing downstream annoation.Originally posted by NextGenSeq View PostComment
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Hi,
When using Bowtie, how to decide which seed length is best?Comment
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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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