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2013-09-16 15:26:36 -0600 answered a question what does "intronic depth" mean in tophat alignment visual?

Good Question!

When sequencing RNA, you are usually looking at post-spliced RNA fragments. These reads don't contain any detailed information about intronic nucleotides because by the time they are sequenced, the intronic RNA has been spliced out. The only thing the aligner can tell us is that the read spans an intron. The intronic depth at a location is the number of reads that span the location, but don't have any sequenced RNA for that region.

So, looking at your example, it seems that 150 out of 172 reads simply skip over the exon in question. This probably means that the exon is poorly expressed and gets spliced out most transcripts. However, in the 22 cases where the exon wasn't spliced out, 20 had a mismatch. I'd say you have some good evidence for a variant, but I'm not sure it's conclusive. A common standard for calling a variant is to have at least 30 reads that support it.

2013-04-03 15:14:15 -0600 answered a question Is there a way to view bases that have been softclipped from reads?

Currently there isn't any way to see soft-clipped bases in the pile-up. The only way to see soft-clipped bases is to click on an alignment and look at the raw sequence in the data console.

We may add an option to draw soft-clipped bases in future versions of GenomeBrowse though, so keep an eye open for updates.

2012-10-04 07:54:05 -0600 received badge  Expert
2012-10-03 13:21:23 -0600 answered a question Examples of Inversions or Rearrangements

Our support for structural variations is currently fairly limited, but here is what we have so far. Note that these require the "Stack Paired-end" option to be enabled. Click the gear menu in the upper left of the pileup plot, and then click "Stack Paired-end".

Mated Pairs:

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Nearby alignments from the same read pair are connected with a thin gray line.

Distant Mated Pairs:

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If a mated pair is separated by more than 1000bp, then they will not be connected with a line. Instead, they will have a small arrow pointing in the direction of their mate. Clicking on the alignment will show a detailed report in the data console which includes more information on the mate. This 1000bp limit exists mostly for technical reasons (pileups get very large and unwieldy with lots of long mated pairs). However, future versions of GenomeBrowse might allow the 1000bp limit to be user-modified.

Chromosome-Spanning Mated Pairs:

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If an alignment's mate is on another chromosome, then a double-headed arrow is drawn pointing in the direction of the mate.

There's been a lot of interest among our users regarding structural rearrangements, so we welcome any suggestions for improvement you might have!

2012-10-02 14:15:24 -0600 answered a question Window size

The actual numeric limit is 8192 bases for pile-up plots (this may change in future versions). But as Gabe mentioned, the limit is removed once the coverage background task finishes.

2012-10-02 14:14:54 -0600 received badge  Associate Editor
2012-10-01 15:11:00 -0600 answered a question Y-axis values

When displaying gene tracks, GenomeBrowse attempts to stack the transcripts in an aesthetically pleasing manner. As a result, the Y values don't have any genomic or scientific meaning. They only represent a transcript's location in that aesthetic arrangement. We debated hiding numeric Y values for gene tracks, but have found that they are sometimes useful for navigation.