Oh, of course. My oversight. Thanks. ---- Original message ---- >Date: Thu, 29 Apr 2010 12:34:55 -0400 >From: Steve Lianoglou <[email protected]> >Subject: Re: [Bioc-sig-seq] ShortRead readAligned Strange Sequences >To: [email protected] >Cc: [email protected] > >Hi, > >On Thu, Apr 29, 2010 at 4:11 AM, Dario Strbenac ><[email protected]> wrote: >> Hello, >> >> I was looking at the first few sequences in the readAligned object >> >> e.g. >> >>> head(sread(aligned)) >> A DNAStringSet instance of length 6 >> width seq >> [1] 36 AACCCTAACCCTAACCCTAACCTTAACCTAACCTTA >> [2] 36 TCCGCCTTCAGAGTACCACCGAAATCTGTGCAGAGG >> [3] 36 GCCTCTCTGCGCCTGCGCCGGCGGCGTTTCGTTCTC >> [4] 36 GCGCGGCGCGCCTCTCGGCGCCTGCGCCGGCGGAGG >> [5] 36 GAGGAAAAAGGCAGGACAGAATTACGAGGTGCTGGC >> [6] 36 GAAAAAGGCAGGACAGAATTACGAGATGCTGGCNCA >> >> and I looked at their strands >> >>> head(strand(aligned)) >> [1] + + - - + + >> >> When I did a search in the .map file relating to this alignment, I was able >> to find the first 2 sequences (which are on the + strand), but not the 3rd, >> nor its complement. Same for the 4th which is also - strand. To get a >> complement I used Biostrings::complementSeq. > >Shouldn't you rather be checking for its reverseComplement? > >-- >Steve Lianoglou >Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University >Contact Info: http://cbio.mskcc.org/~lianos/contact
-------------------------------------- Dario Strbenac Research Assistant Cancer Epigenetics Garvan Institute of Medical Research Darlinghurst NSW 2010 Australia _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
