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Any programs for analyzing solexa transcriptome (alternative splicing) ?
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Do you have a reference transcriptome?Originally posted by baohua100 View Post
If so, does it contain alternatively spliced sequences? -
we have reference transcriptome 。 but one gene one transcript sequence
there are no alternative splicing informationComment
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I wonder if Solexa reads, say 50bp can identify alternative splicing when you don't have a reference genome. How can we tell the alignment software to map the reads so we can find splice variant?
Alternative splicing has been reported using 454 reads. The longer reads is probably an advantage. Anyone has done similar work using Solexa reads?Comment
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Tophat does a really nice job mapping splice junctions without a set of known splice sites. It works very well with short Solexa reads, though I presume it requires a certain degree of read depth.Comment
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i have reads.fq (5 000 000 reads RNA-seq) genome.fa
when i use bowtie align the reads, it aligns 4 200 000 reads.
but when i use tophat align the reads, the output file accepted_hits.sam only contains 1 900 000 reads. junctions.bed file is blank.Comment
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Gmorse from the french genoscope (PMID: 19087247). It works with short reads and does not require any reference transcriptome, as explained here. Maybe limited for very complex and dense transcriptomes though (human/mouse/etc).Originally posted by baohua100 View Post
With a reference transcriptome, if you want to assign a quantity to each splicing variant I only know about this flux capacitor. Maybe not fully stable yet. I'm sure a lot of similar projects are in progress.
(Disclaimer: I personally know these people, they are friends of mine -but don't worry, contrary to me they still work in academic research).
Much more is expected to come from the RGASP project. I'd suggest to keep an eye on this.
Then, there are commercial products that claim to address "alternative splicing", but I am curious about what they really do...
yours,
s.Comment
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
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
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