STAR vs Novoalign IGV Browser visualization
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10 weeks ago
chasem ▴ 10

I feel a bit silly about this, but I'm having trouble finding information on the horizontal lines which appear with STAR alignments, but not novoalign alignments. Could anyone help point me in the right direction for documentation on what these mean?

These are single end reads from the same rnaseq library.

IGV STAR vs Novoalign alignments

browser IGV novoalign genome STAR • 453 views
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The lines across splice junctions make sense. It is the long ones -- the ones that span the chromosome -- which I'm concerned about.

Edit: novoalign (or at least not in the way that I am running it -- it may have a setting for splices, not sure) is not splice aware, which I realize is obvious, so of course there are no splices in the bottom track. It is really just the long gaps that are catching my attention here.

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Do you expect translocations like that to be present in your data?

single end reads from the same rnaseq library

This makes their presence even more unusual.

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I was not expecting this -- not sure what to make of it yet.

That said, I did end up reading the STAR documentation more closely. This time, I noticed that there is a setting to set the max intron length. I am going to try setting that to some multiple of the longest intron to see what happens.

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I see those ridiculously long spliced reads in just about every STAR alignment I do. I would be aware of them but ignore them.

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sounds like IGV doesn't understand something from the latest STAR bams. would be interested to see if an older STAR version does this.

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For me it seems to be a just a very common artifact - reads that are spliced incredibly far.

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That is good to know that it isn't just my set of reads...still concerning, though.

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