I am trying to intersect methylation data with promoter.bed. This promoter file I made from UCSC refseq gene and gene prediction.bed.
1 chr1 134212401 134213001 NM_001195025 0 +
2 chr1 134212401 134213001 NM_028778 0 +
3 chr1 8349519 8350119 NM_001290392 0 -
4 chr1 8349519 8350119 NM_001290390 0 -
5 chr1 8349519 8350119 NM_027671 0 -
6 chr1 33510352 33510952 NM_008922 0 -
7 chr1 25124020 25124620 NM_175642 0 -
8 chr1 8349519 8350119 NM_001290393 0 -
9 chr1 58714664 58715264 NM_175370 0 -
10 chr1 75482099 75482699 NM_178884 0 -
11 chr1 125228414 125229014 NM_199021 0 -
12 chr1 109050237 109050837 NM_198680 0 -
13 chr1 75492612 75493212 NM_001310679 0 -
14 chr1 167718511 167719111 NM_001113391 0 +
15 chr1 184494837 184495437 NM_130890 0 +
16 chr1 176102606 176103206 NM_011465 0 +
17 chr1 167718511 167719111 NM_031162 0 +
18 chr1 167718511 167719111 NM_001113393 0 +
19 chr1 167718511 167719111 NM_001113392 0 +
20 chr1 167718511 167719111 NR_103716 0 +
after intersection i calculated the average methylation of each unique id .
When i merge the files to get methylation from each file in a single file having the ids and methylation column from each file, it shows the duplication after record number 7725 as follow:
gene chr str end file1 file2
NR_002841 chr6 47604619 47605219 100 100
NR_002841 chr6 47604619 47605219 100 100
NR_002841 chr6 47604619 47605219 100 100
NR_002841 chr6 47621924 47622524 100 100
NR_002841 chr6 47621924 47622524 100 100
NR_002841 chr6 47621924 47622524 100 100
NR_002841 chr6 47621924 47622524 100 100
NR_002841 chr6 47621924 47622524 100 100
i dont know why it is doing like this. although i am using a merge function that worked well uptil merging of 10 files but after it i am having problem like this:
Interestingly, dupplicated regions also include(same id different strt and end sites):
NR_002841 chr6 47621924 47622524 100 100
NR_002841 chr6 47604619 47605219 100 100
NR_002841 chr6 47604619 47605219 100 100
NR_002841 chr6 47621924 47622524 100 100
NR_002841 chr6 47621924 47622524 100 100
NR_002841 chr6 47604619 47605219 100 100
NR_002841 chr6 47604619 47605219 100 100
NR_002841 chr6 47608940 47609540 100 100
NR_002841 chr6 47608940 47609540 100 100
NR_002841 chr6 47604619 47605219 100 100
NR_002841 chr6 47604619 47605219 100 100
NR_002841 chr6 47604619 47605219 100 100
Are you using bedtools?
if you use bedtools intersect note that there is the option " -u". Please provide what you are using to merge the files, otherwise it is again hard to imagine what exactly you are doing.
chr12 112996778 112997378 NM_001025363 0 +
chr12 112996778 112997378 NM_001025362 0 +
chr12 112996778 112997378 NM_001025361 0 +
chr12 112996778 112997378 NM_001025359 0 +
chr12 112996778 112997378 NM_001025358
I used intersect -u command but it again gave differnt ids against same location of chr.
above is the output of the command.What should I do now?
This looks correct to me. You get only unique matches, right?
Or do you want the number of matches in that region? (parameter: -c )
What exactly do you want to have? Could you write one line or two by hand? There are also other options to address what should be reported from file A or B.
here u can see same chr same location differnt ids.
I want to get a unique id for single location of chr.
but every time i am getting outputs like below(last column is average,ignore that):
NM_001081463 chr5 134833230 134833830 0 - 12.5
NM_001081464 chr5 134833230 134833830 0 - 12.5
NM_001081465 chr5 134833230 134833830 0 - 12.5
NM_001081466 chr5 134833230 134833830 0 - 12.5
NM_001081467 chr5 134833230 134833830 0 - 12.5
NM_001081468 chr5 134833230 134833830 0 - 12.5
NM_001081469 chr5 134833230 134833830 0 - 12.5
NM_001081470 chr5 134833230 134833830 0 - 12.5
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