Hi Joseph,
Joseph Dhahbi, P.h.D. wrote:
Hi
I downloaded the drosophila RepeatMasker from UCSC GB as a text file
which is in fasta format and looks like this:
dm3_rmsk_NINJA_I range=chr4:2-434 5'pad=0 3'pad=0 strand=+
repeatMasking=none
AATTCGCGTCCGCTTA......
dm3_rmsk_NINJA_LTR range=chr4:435-611 5'pad=0 3'pad=0 strand=+
repeatMasking=none
TGTCGCGGATC....
dm3_rmsk_Baggins1 range=chr4:638-1723 5'pad=0 3'pad=0 strand=-
repeatMasking=none
ATACGATGG......
I made the input dictionary and I would like to make the RepeatMasker
sequences as the target. When I used ‘read.DNAStringSet’ it recognized
only the first sequence of the fasts file. Ho do I merge all of the
sequences in and make them as a target.
If your file is really FASTA then read.DNAStringSet() should extract all
the records and return a DNAStringSet object where each element corresponds
to a record in the original file. So it seems like you've hit a bug in the
read.DNAStringSet() function. Can you please provide the URL to the file
you downloaded so we can try to reproduce?
Anyway, what you are trying to achieve can be done in an easier (and more
efficient) way. You don't need to download the RepeatMasker sequences for
this; just use the BSgenome.Dmelanogaster.UCSC.dm3 package. The RepeatMasker
information is already included in it as part of the built-in masks provided
for each chromosome:
> library(BSgenome.Dmelanogaster.UCSC.dm3)
> Dmelanogaster
Fly genome
|
| organism: Drosophila melanogaster
| provider: UCSC
| provider version: dm3
| release date: Apr. 2006
| release name: BDGP Release 5
|
| single sequences (see '?seqnames'):
| chr2L chr2R chr3L chr3R chr4 chrX chrU
| chrM chr2LHet chr2RHet chr3LHet chr3RHet chrXHet chrYHet
| chrUextra
|
| multiple sequences (see '?mseqnames'):
| upstream1000 upstream2000 upstream5000
|
| (use the '$' or '[[' operator to access a given sequence)
> chr2L <- Dmelanogaster$chr2L
> chr2L
23011544-letter "MaskedDNAString" instance (# for masking)
seq:
CGACAATGCACGACAGAGGAAGCAGAACAGATATTT...GCATATTTGCAAATTTTGATGAACCCCCCTTTCAAA
masks:
maskedwidth maskedratio active names
1 200 8.691290e-06 FALSE assembly gaps
2 1966561 8.545976e-02 FALSE RepeatMasker
3 61603 2.677048e-03 FALSE Tandem Repeats Finder [period<=12]
all masks together:
maskedwidth maskedratio
1988181 0.08639929
all active masks together:
maskedwidth maskedratio
0 0
Note that the built-in masks are always inactive by default. To activate
a mask do:
> active(masks(chr2L))[2] <- TRUE # activate the RepeatMasker mask
Now only the parts of chr2L that are NOT repeat regions are visible.
To invert this, use gaps():
> chr2Lrepeats <- gaps(chr2L)
> chr2Lrepeats
23011544-letter "MaskedDNAString" instance (# for masking)
seq:
#GACAATGCACGACAGAGGAAGCAGAACAGATATTT...GCATATTTGCAAATTTT###################
masks:
maskedwidth maskedratio active
1 21044983 0.9145402 TRUE
Then use matchPDict() (or countPDict()) in the usual way.
The GenomeSearching vignette in the BSgenome package has more
information about masking (some sections are still incomplete but
will be completed soon).
Hope this helps,
H.
Thank you for your help
Regards,
Joseph
Joseph M. Dhahbi, PhD
Childrens Hospital Oakland Research Institute
5700 Martin Luther King Jr. Way
Oakland, CA 94609
USA
Ph.(510)428-3885 EXT.5743
Cell.(702)335-0795
Fax (510)450-7910
[EMAIL PROTECTED]
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