[Bioc-sig-seq] filtering adaptors again
Martin Morgan
mtmorgan at fhcrc.org
Thu Mar 26 20:27:57 CET 2009
"Lana Schaffer" <schaffer at scripps.edu> writes:
> 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]
clean(fq4) != fq4, so if this is your code you're subsetting the wrong
object.
Martin
> [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
> schaffer at scripps.edu
>
> _______________________________________________
> Bioc-sig-sequencing mailing list
> Bioc-sig-sequencing at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M2 B169
Phone: (206) 667-2793
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