[miso-users] Events with many gene annotations
Sol Katzman
solkatzman at sbcglobal.net
Wed Aug 28 17:53:41 EDT 2013
Attached are the distributions (and the script used to generate them).
/Sol.
On 8/28/2013 2:51 PM, Sol Katzman wrote:
> Dear Yarden and Tyler,
>
> A while back, I noticed some performance problems processing AFE/ALE events.
>
> I extracted the distributions of the lengths of the "gene" items in the gff3
> (hg19) event definitions. There are many (1100+/500+) AFE/ALE events over 1Mb in length.
> Only a handful (10) such SE events.
>
> I will send my stats in a follow-up email.
>
> I think that the events longer than 1Mb are pretty questionable.
>
> /Sol.
>
> On 8/28/2013 2:16 PM, Tyler Funnell wrote:
>> Hi Yarden,
>>
>> Yes that's right. The problem is most noticeable for the ALE/AFE events for the reason you mentioned, but I think the current
>> event to gene mapping could have improper annotations for other event types as well. For example, small genes that exist within
>> the introns in a SE event would be picked up.
>>
>> Cheers,
>> Tyler
>>
>>
>> On Aug 28, 2013, at 2:03 PM, Yarden Katz <yarden at mit.edu> wrote:
>>
>>> Hi Tyler,
>>>
>>> Some of the AFE/ALE annotations, which we are currently reworking, have span very large genomic coordinates as you noted. I
>>> believe these are probably dubious/faulty annotations. But in any case, as you say, if you overlap the outer-most coordinates
>>> with genes there will potentially be many overlapping genes.
>>>
>>> If I understand correctly, you're proposing to merge the first exon with all genes, then the second exon will genes, and take
>>> the intersection of those?
>>>
>>> Best, --Yarden
>>>
>>> On Aug 27, 2013, at 10:31 PM, Tyler Funnell wrote:
>>>
>>>> Hello,
>>>>
>>>> I've noticed that for some alternative events, there are many gene annotations in the event to ensembl Id mapping file. For
>>>> example AFE event 83896 at uc002kgt.1@uc002hvt.1 has quite a few. I think this might be because the left-most and right-most
>>>> coordinates for this particular event cover a large section of the chromosome and the gene mappings are based on these
>>>> coordinates. If I'm right, I think a better way would be to get the overlap between genes (or gene exons) and individual event
>>>> exons first, then merge to the event level.
>>>>
>>>> Thank you,
>>>> Tyler
>>>>
>>>>
>>>> _______________________________________________
>>>> miso-users mailing list
>>>> miso-users at mit.edu
>>>> http://mailman.mit.edu/mailman/listinfo/miso-users
>>>
>>
>>
>> _______________________________________________
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>>
>
-------------- next part --------------
set genome = hg19
set gffDir = /hive/groups/wet/illumina/geneModels/${genome}/miso_gff/${genome}
set eventList = (AFE ALE A3SS A5SS MXE SE TandemUTR RI)
cd $gffDir
foreach ae ($eventList)
set gffName = ${ae}.${genome}.gff3
echo "--------------------------------------------"
echo "stats for lengths (in kb) of gene items in event gff"
echo "gffDir: $gffDir"
echo "gffName: $gffName"
cat $gffDir/$gffName | \
gawk '($3 == "gene")' | \
cut -f 4,5 | \
gawk '{print ($2 - $1)/1000}' \
> temp.${ae}.lengths
echo ""
cat temp.${ae}.lengths | ave stdin
echo ""
cat temp.${ae}.lengths | textHistogram -binSize=100 stdin
rm -f temp.${ae}.lengths
end
--------------------------------------------
stats for lengths (in kb) of gene items in event gff
gffDir: /hive/groups/wet/illumina/geneModels/hg19/miso_gff/hg19
gffName: AFE.hg19.gff3
Q1 11.718500
median 36.585000
Q3 118.308250
average 2235.596544
min 0.061000
max 242543.000000
count 19720
total 44085963.849000
standard deviation 11335.026775
large values truncated: need 2425 bins or larger binSize than 100
Maximum value 242543.000000
0 ************************************************************ 14282
100 ********* 2219
200 ***** 1079
300 ** 374
400 * 167
500 117
600 72
700 119
800 46
900 27
1000 14
1100 9
1200 6
1300 9
1400 11
1500 35
1600 7
1700 2
1800 6
1900 5
2000 9
2100 0
2200 1
<minVal or >=2300 ***** 1104
--------------------------------------------
stats for lengths (in kb) of gene items in event gff
gffDir: /hive/groups/wet/illumina/geneModels/hg19/miso_gff/hg19
gffName: ALE.hg19.gff3
Q1 7.085000
median 19.504000
Q3 60.781000
average 2011.638801
min 0.229000
max 242515.000000
count 10269
total 20657518.843000
standard deviation 9984.357978
large values truncated: need 2425 bins or larger binSize than 100
Maximum value 242515.000000
0 ************************************************************ 8395
100 ***** 742
200 ** 325
300 * 78
400 48
500 28
600 26
700 32
800 21
900 5
1000 8
1100 1
1200 2
1300 4
1400 8
1500 7
1600 3
1700 0
1800 0
1900 2
2000 7
<minVal or >=2100 **** 527
--------------------------------------------
stats for lengths (in kb) of gene items in event gff
gffDir: /hive/groups/wet/illumina/geneModels/hg19/miso_gff/hg19
gffName: A3SS.hg19.gff3
Q1 0.873250
median 1.723000
Q3 3.936750
average 13.790749
min -2.440000
max 90101.800000
count 14960
total 206309.608000
standard deviation 737.490719
large values truncated: need 901 bins or larger binSize than 100
Maximum value 90101.000000
0 ************************************************************ 14769
100 34
200 13
300 * 128
400 8
500 3
600 2
700 0
800 0
900 1
<minVal or >=1000 2
--------------------------------------------
stats for lengths (in kb) of gene items in event gff
gffDir: /hive/groups/wet/illumina/geneModels/hg19/miso_gff/hg19
gffName: A5SS.hg19.gff3
Q1 0.838000
median 1.730000
Q3 3.620000
average 4.084345
min -22.779000
max 529.531000
count 12807
total 52308.207000
standard deviation 13.678279
0 ************************************************************ 12778
100 17
200 4
300 2
400 4
500 1
<minVal or >=600 1
--------------------------------------------
stats for lengths (in kb) of gene items in event gff
gffDir: /hive/groups/wet/illumina/geneModels/hg19/miso_gff/hg19
gffName: MXE.hg19.gff3
Q1 6.725000
median 15.607000
Q3 37.239000
average 38.464499
min 0.475000
max 932.967000
count 2723
total 104738.831000
standard deviation 73.946593
0 ************************************************************ 2515
100 *** 119
200 * 32
300 * 28
400 13
500 12
600 2
700 0
800 0
900 2
--------------------------------------------
stats for lengths (in kb) of gene items in event gff
gffDir: /hive/groups/wet/illumina/geneModels/hg19/miso_gff/hg19
gffName: SE.hg19.gff3
Q1 3.207000
median 6.770000
Q3 15.346750
average 20.210842
min -22.779000
max 90101.500000
count 39232
total 792911.753000
standard deviation 643.883559
large values truncated: need 901 bins or larger binSize than 100
Maximum value 90101.000000
0 ************************************************************ 38473
100 * 574
200 110
300 46
400 7
500 7
600 3
700 0
800 1
900 0
1000 1
<minVal or >=1100 10
--------------------------------------------
stats for lengths (in kb) of gene items in event gff
gffDir: /hive/groups/wet/illumina/geneModels/hg19/miso_gff/hg19
gffName: TandemUTR.hg19.gff3
Q1 0.679250
median 1.188000
Q3 2.036500
average 1.548208
min 0.109000
max 12.567000
count 2656
total 4112.041000
standard deviation 1.224639
0 ************************************************************ 2656
--------------------------------------------
stats for lengths (in kb) of gene items in event gff
gffDir: /hive/groups/wet/illumina/geneModels/hg19/miso_gff/hg19
gffName: RI.hg19.gff3
Q1 0.366000
median 0.555000
Q3 1.052250
average 0.862697
min 0.076000
max 9.694000
count 5986
total 5164.105000
standard deviation 0.822856
0 ************************************************************ 5986
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