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Individual read alignments within GWIPS?
02-Oct-2014, 12:49 PM
Post: #1
Individual read alignments within GWIPS?
Question and response below about viewing the individual read alignments within GWIPS:

I enjoyed reading your NAR paper describing GWIPS-viz. I wonder if there is a way to view the individual read alignments within GWIPS? There are isoforms of genes that differ in their exon-exon connectivity and translation can only be confirmed if there is a ribosomal footprint crossing the isoform-specific splice junction. The example listed in figure 2 shows an isoform that has a novel exon, which is only a subset of all splice forms.

Much thanks,
Gloria




Response:

Dear Gloria

I confirm that we do not provide the actual sequence reads in GWIPS-viz. However, the alignment information can be downloaded from the Table Browser. This might help if you wish to check for exon specific footprint alignments (enter the coordinates of the exon in the format chrX:aaaa-zzzzz in the position box) and get the output.
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