Changes between Initial Version and Version 1 of BIOS_ReferenceFiles/MetaExonAnnotation-05-06-13


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Timestamp:
Sep 19, 2016 4:47:16 PM (22 months ago)
Author:
jamverlouw
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  • BIOS_ReferenceFiles/MetaExonAnnotation-05-06-13

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     1= Meta-exon annotation 05-06-13 =
     2
     3To create the meta-exon annotation we merged all overlapping exons from Ensembl version 71 (see [FgReferenceFiles Transcript annotation section]) using mergeBed tool from BEDTools suite. Overlapping exons belonging to different genes or different strands were also merged into one meta-exon. This was done using the commands described in [wiki:FgReferenceFiles/MetaExonAnnotation_documentation Meta-exon annotation documentation]
     4
     5Location: `srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/RP3/dzhernakova/meta-exons_v71_cut_sorted_05-06-13.gtf.gz`[[BR]]
     6Contact: `dasha.zhernakova@gmail.com`
     7
     8
     9== Issue: overlapping exons ==
     10
     11The meta-exon annotation 05-06-13 track incorrectly contains some overlapping exons. Since this problem was only detected after the first freeze, all exon and gene counts for the freeze are still based on this track. We may correct the track in the future for later pipeline runs.
     12
     13As an example, the following two entries are in the track:
     14{{{
     15MT 10470 10766
     16MT 10760 12137
     17}}}
     18However, they overlap, which should never be the case.
     19
     20In the complete meta-exon annotation, 269 such regions were identified, originating from 730 exons which are not properly merged, all of them on MT and X chromosomes. You can easily do the same check with `bedtools intersect -n` on the meta exon track. This was solved by removing additional contigs(GL*, LRG* etc) from the Ensembl Biomart export before merging.
     21
     22Affected exons (730) are attached (and could be used as a blacklist): [raw-attachment:meta-exons_v71_cut_sorted_05-06-13.unmerged.bed meta-exons_v71_cut_sorted_05-06-13.unmerged.bed]