Error in CountOverlaps

[biofreak]

hi
I get the following error when I run:
countOverlaps(exonRangesListtx[[hif1Ind[r]]], align)

In .Seqinfo.mergexy(x, y) :
Each of the 2 combined objects has sequence levels not in the other:
- in 'x': 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, X, Y, MT, MG153_PATCH, MG3835_PATCH, MG4136_PATCH, MG4151_PATCH, MG4209_PATCH, MG4211_PATCH, MG4212_PATCH, MG4213_PATCH, MG4214_PATCH, GL456210.1, GL456211.1, GL456212.1, GL456213.1, GL456216.1, GL456219.1, GL456221.1, GL456233.1, GL456239.1, GL456350.1, GL456354.1, GL456359.1, GL456360.1, GL456366.1, GL456367.1, GL456368.1, GL456370.1, GL456372.1, GL456378.1, GL456379.1, GL456381.1, GL456382.1, GL456383.1, GL456385.1, GL456387.1, GL456389.1, GL456390.1, GL456392.1, GL456393.1, GL456394.1, GL456396.1, JH584292.1, JH584293.1, JH584294.1, JH584295.1, JH584296.1, JH584297.1, JH584298.1, JH584299.1, JH584300.1, JH584301.1, JH584302.1, JH584303.1, JH584304.1
- in 'y': chr1, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chrM, chrX, chrY
Make sure to always combine/compare [... truncated] "


The two objects are as follows:
1) exonRangesListtx[[hif1Ind[r]]]
GRanges with 15 ranges and 3 elementMetadata cols:
seqnames ranges strand | exon_id exon_name exon_rank
<Rle> <IRanges> <Rle> | <integer> <character> <integer>
[1] 12 [73907904, 73908324] + | 76987 ENSMUSE00000405171 1
[2] 12 [73926557, 73926747] + | 310532 ENSMUSE00001223008 2
[3] 12 [73927986, 73928131] + | 4438 ENSMUSE00000114679 3
[4] 12 [73928214, 73928298] + | 4437 ENSMUSE00000114678 4
[5] 12 [73930657, 73930769] + | 4442 ENSMUSE00000114690 5
[6] 12 [73932274, 73932476] + | 4440 ENSMUSE00000114682 6
[7] 12 [73936190, 73936296] + | 4441 ENSMUSE00000114687 7
[8] 12 [73937653, 73937800] + | 4443 ENSMUSE00000114695 8
[9] 12 [73939529, 73939749] + | 4444 ENSMUSE00000114697 9
[10] 12 [73940348, 73940631] + | 4439 ENSMUSE00000114680 10
[11] 12 [73941688, 73941852] + | 52364 ENSMUSE00000297829 11
[12] 12 [73941961, 73942385] + | 4445 ENSMUSE00000114699 12
[13] 12 [73944079, 73944187] + | 4435 ENSMUSE00000114675 13
[14] 12 [73944911, 73945037] + | 4436 ENSMUSE00000114677 14
[15] 12 [73945552, 73947530] + | 68877 ENSMUSE00000369537 15
---
seqlengths:
1 2 3 4 5 6 7 8 ... JH584298.1 JH584299.1 JH584300.1 JH584301.1 JH584302.1 JH584303.1 JH584304.1
195471971 182113224 160039680 156508116 151834684 149736546 145441459 129401213 ... 184189 953012 182347 259875 155838 158099 114452
>


2)aligns:
GappedAlignments with 1020 alignments and 0 elementMetadata cols:
seqnames strand cigar qwidth start end width ngap
<Rle> <Rle> <character> <integer> <integer> <integer> <integer> <integer>
[1] chr12 * 50M 50 73907984 73908033 50 0
[2] chr12 * 50M 50 73907985 73908034 50 0
[3] chr12 * 50M 50 73908016 73908065 50 0
[4] chr12 * 50M 50 73908032 73908081 50 0
[5] chr12 * 50M 50 73908039 73908088 50 0
[6] chr12 * 50M 50 73908043 73908092 50 0
[7] chr12 * 50M 50 73908081 73908130 50 0
[8] chr12 * 50M 50 73908084 73908133 50 0
[9] chr12 * 50M 50 73908084 73908133 50 0
... ... ... ... ... ... ... ... ...
[1012] chr12 * 50M 50 73947246 73947295 50 0
[1013] chr12 * 50M 50 73947248 73947297 50 0
[1014] chr12 * 50M 50 73947268 73947317 50 0
[1015] chr12 * 50M 50 73947284 73947333 50 0
[1016] chr12 * 50M 50 73947325 73947374 50 0
[1017] chr12 * 50M 50 73947358 73947407 50 0
[1018] chr12 * 50M 50 73949633 73949682 50 0
[1019] chr12 * 50M 50 73949656 73949705 50 0
[1020] chr12 * 50M 50 73949680 73949729 50 0
---
seqlengths:
chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 ... chr4 chr5 chr6 chr7 chr8 chr9 chrM chrX chrY
195471971 130694993 122082543 120129022 120421639 124902244 104043685 98207768 94987271 90702639 ... 156508116 151834684 149736546 145441459 129401213 124595110 16299 171031299 91744698



Can someone please help?
thanks a lot.

[Wolfgang Huber]

Dear Biofreak

did you notice that the naming of the chromosomes ('sequence levels' in Bioconductor jargon) is different in the two objects that you are trying to overlap? The first uses '1, 2, 3, 4, 5, ...', the second 'chr1, chr10, chr11, chr12,....'. The software is not yet clever enough to repair that for you. You will need to unify the naming before calling 'countOverlaps'.

This exact question has been extensively discussed on the Bioconductor mailing list, and search engines will readily show up these threads for you. If questions remain, consider posting project-specific, technical questions to the Bioconductor mailing list, as tje response there may be wider and faster, and please also follow their posting guide, in particular, provide a reproducible example (that someone else besides you can run) and the version numbers (output of 'sessionInfo()').

Best wishes
Wolfgang