Hi Lana,
Have you tried using the "trimLRPatterns" function?
I usually start with a small part of the primer, say the first ~10
bases, padded by Ns to make up a read of full length.
Cheers,
Cei
Lana Schaffer wrote:
Hi,
I have read Feb 2009 archives and have been trying to
filter alot of primer reads to see what I short reads
remaining.
The small RNA primer (TCGTATGCCGTCTTCTGCTTG) attached to
a series of A's is most contamination of the reads that
I would like to filter.
-------------------------------------------------------
dist1 <- srdistance(clean(fq4), "TCGTATGCCGTCTTCTGCTTGAAAAAAAAAA")
table(dist1[[1]])
4 5 6 7 8 9 10 11 12 13 14 15 16 17
18 19
9338 789 406 121 2094 240 184 55 332 78 90 25 68 16
62 31
20 21 22 23 24 25 26 28 29
166 550 623 640 318 65 6 1 4
f <- fq4[dist1[[1]] <5]
[1] 35 NTAGTACTCTGCGTTGTGGCCGCAGCCACCTCGGT
[2] 35 NTCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAA
[3] 35 NTCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAA
[4] 35 NTCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAA
[5] 35 NCTGGACTTGGAGTCAGAAGATCTCGTATGCCGTC
[6] 35 NTCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAA
[7] 35 GGTATGATTCTCGCATCTCGTATGCCGTCTTCTGC
[8] 35 GGTATGATTCTCGCATCTCGTATGCCGTCTCCTGC
[9] 35 ATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAA
... ... ...
[9363] 35 TCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAA
[9364] 35 ATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAA
[9365] 35 TCGTATGCCGTCTTCTGCTTGAAAAAAAAAAACAA
[9366] 35 ATATAATACAACCTGCTAAGTGATCTCGTATGCCG
[9367] 35 ATCTCGTATGCCGTCTTCTGCTTGACAAAAAAAAA
[9368] 35 ATCTCGTATGCCGTCTTCTGCTTGAAAAACAACAA
[9369] 35 ATCTCGTATGCCGTCTTCTGCTTGAACCACACAAA
[9370] 35 GTATGCCGTCTTCTGCTTGAAAAAAAAAAAAACCA
[9371] 35 ATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAA
f <- fq4[dist1[[1]] >28]
[1] 35 ATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAA
[2] 35 CGATCATCTCGTATGCCGTCTTCTGCTTGAAAAAA
[3] 35 GTATGCCGTCTTCTGCTTGAAAAAAAAAAACAACC
[4] 35 CAGCAATCTCGTATGCCGTCTTCTGCTTGAAAAAA
---------------------------------------------------------
You can see that I am not doing a good filtering job.
d<5 is showing some sequences free of primer that I would
want to save.
I have tried the polyn function, but that does not work for me
when I use a series of 10-20 A's (<35).
Would someone be able to give me some suggestions?
sessionInfo()
R version 2.9.0 Under development (unstable) (2009-02-12 r47905)
i386-pc-mingw32
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ShortRead_1.1.50 lattice_0.17-20 BSgenome_1.11.9
Biostrings_2.11.42
[5] IRanges_1.1.54
loaded via a namespace (and not attached):
[1] Biobase_2.3.11 grid_2.9.0 hwriter_1.1
Matrix_0.999375-20
Lana Schaffer
Biostatistics/Informatics
The Scripps Research Institute
DNA Array Core Facility
La Jolla, CA 92037
(858) 784-2263
(858) 784-2994
[email protected]
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