I want to create a library for all possible exons in a gene for a human gene. This is not possible by gtf file which is available in Ensembl. Because I want to create mRNA of all possible combinations of exons and also exons and introns. I saw various platforms to searching this but didn't get any hit. So please can anyone help me to sort this. Thanks in advance.
I download the coordinates of all exons from biomart: It contains 5 columns 1st three are chromosome no., start exon, end exon. 4th column is transcript id, 5th column is exon rank.
10 100009838 100009947 ENST00000324109 1
10 99875577 99877336 ENST00000324109 17
10 99879811 99880361 ENST00000324109 16
10 99884011 99884209 ENST00000324109 15
10 99885687 99885866 ENST00000324109 14
10 99886300 99886632 ENST00000324109 13
10 99888825 99888953 ENST00000324109 12
10 99894946 99895050 ENST00000324109 11
10 99896267 99896397 ENST00000324109 10
10 99898086 99898285 ENST00000324109 9
10 99898743 99898760 ENST00000324109 8
10 99899919 99900066 ENST00000324109 7
10 99907995 99908094 ENST00000324109 6
10 99908953 99909146 ENST00000324109 5
10 99955214 99957205 ENST00000324109 4
10 99969115 99969237 ENST00000324109 3
10 99971980 99972134 ENST00000324109 2
10 100042193 100042573 ENST00000370418 9
10 100048758 100048876 ENST00000370418 8
10 100054347 100054446 ENST00000370418 7
10 100057013 100057152 ENST00000370418 6
10 100063614 100063725 ENST00000370418 5
10 100065188 100065370 ENST00000370418 4
10 100069714 100069869 ENST00000370418 3
10 100075911 100076107 ENST00000370418 2
10 100081403 100081869 ENST00000370418 1
So by these coordinates file can I make all possible combinations of whole genes and get in fasta format with different names.
Thanks in advance
Related
I'm working on creating Google Charts from MySQL datasource. This works fine so far. Now I want to count how many blocks of a Blockchain processed per hour.
How can I simple substract the first row from last row of a group?
SELECT
date_format(time,'%Y-%m-%d %H-%i'),blocks,
count(1)
FROM blockchain
GROUP BY 1
ORDER BY `date_format(time,'%Y-%m-%d %H-%i')` ASC
And if this done, how to repeat this for the last 24 hours?
Sample data:
id time blocks
3 2020-12-30 11:21:53 112149
4 2020-12-30 11:21:55 112150
5 2020-12-30 11:21:56 112150
6 2020-12-30 11:21:57 112150
7 2020-12-30 11:24:01 112169
8 2020-12-30 11:25:01 112178
9 2020-12-30 11:26:01 112188
10 2020-12-30 11:27:01 112197
-10 2020-12-30 11:27:01 112197
3 2020-12-30 11:21:53 112149
-----------------------------------------------
48
I hope its not a stupid question. I'm kinda new to this.
You can use this query to get blocks per hour.
select hour(time) as hr, max(blocks)-min(blocks) as blocks_per_hour
from test
group by hour(time)
Result:
hr
blocks_per_hour
11
48
Example:
https://dbfiddle.uk/?rdbms=mysql_5.7&fiddle=96ee323e8f15af0a946ff1220af01588
i have following sample database:
date open_price closed_price
25/1/19. 6 10
24/1/19 10 12
23/1/19 8 7
22/1/19 9 4
21/1/19 4 12
20/1/19 7 16
.....
so would be possible to use sql /mysql to create another column and calculate average open_price of every 3 days automatically with following display:
date open_price closed_price avg(3)
25/1/19. 6 10 8
24/1/19 10 12 9
23/1/19 8 7 7
22/1/19 9 4 7
21/1/19 4 12
20/1/19 8 16
.....
Why do you need to use an extra field for that?
You can always to calculate that data in your sql query
SELECT *, (open_price+closed_price)/2 as avg_price
FROM `test_price`
i have a table :
a b c
1 10 1001
7 6 54
56 2000 31
1200 5 9
4 10 20
2 65 20
how can i select rows with column's value of this row smaller than 1000. i want to get this
a b c
7 6 54
4 10 20
2 65 20
mysql query still get all value :
SELECT a,b,c FROM test
where a <'1000' or b<'1000' or c<'1000'
It sounds like you would like to pull a row where there is NO column greater than 1000 in that row, if that is correct then you need to us AND instead of OR.
SELECT a,b,c FROM test
where a <'1000' AND b<'1000' AND c<'1000'
Hope that helps!
The graph consists of more than three million nodes and more than 20 million edges. I'm using igraph package on a 8G RAM linux server. The code is
cliques(g,min=3,max=3)
After six days passed, the code is still running. Is there a better way to find all the triples in a graph?
Following #GaborCsardi suggestion you can see this simple example (I used http://igraph.org/nightly igraph dev version)
kite <- graph.famous("Krackhardt_Kite")
triangles(kite)
which yields:
[1] 4 1 2 4 1 3 4 2 5 4 6 1 4 6 3 4 6 7 4 7 2 4 7 5 6 1 3 6 7 8 7 2 5
for the (undirected) graph "Krackhardt_Kite"
You can compare the results with
plot(kite)
Hope this helps
Considering the following table
I have a large table from which I can query to get the following table
type no of times type occurs
101 450
102 562
103 245
111 25
112 28
113 21
Now suppose I wanted to get a table which shows me the sum of no of times type occurs
for type starting with 1 then starting with 10,11,12,13.......19 then starting with 2, 20,21, 22, 23...29 and so on.
Something like this
1 1331 10 1257
11 74
12 ..
13 ..
.. ..
2 ... 20 ..
21 ..
Hope I am clear
Thanks
You really have two different queries:
SELECT [type]\100 AS TypePart, Count(t.type) AS CountOftype
FROM t
GROUP BY [type]\100;
And:
SELECT [type]\100 AS TypePart, [type] Mod 100 AS TypeEnd,
Count(t.type) AS CountOftype
FROM t
GROUP BY [type]\100, [type] Mod 100;
Where t is the name of the table.
Here on the first query i am getting something like this
utypPart CountOftype
1 29
2 42
3 46
4 50
5 26
6 45
7 33
9 1
it is giving me how many utyp are starting with 1 2 and so on
but whai i want is the sum of no of times those types occur for the utyp .