Computational biology and genomics
Updated on the 31st May 2013 and updated again on the 25th March 2015 in light of Chris’s comment. RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. Results of RepeatMasker performed on the human and mouse genomes are provided via the UCSC Table Browser tool. In the…
Updated 2014 June 8th I first tried this with BWA. Now I’ll try it with Bowtie. Consider this reference sequence, which is the sequence “ACGTACGTACGTACGTAGGTACGTAGGG” repeated 20 times: >artificial ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG and this read: >tag ACGTACGTACGTACGTAGGTACGTA The…
2014 June 6th: Major rewrite of post The Burrows-Wheeler Aligner (BWA) is a popular short read alignment program. Here I test the program with an artificial reference sequence. First download and compile the program:
Lincoln Stein has written a bunch of modules to deal with SAM/BAM files. Check out the CPAN module. If you are having trouble installing Bio::DB::Sam, you may have to recompile SAMTools with the following command: To install the Perl module on a machine where you don’t have root access, follow these instructions. Using this module,…
Split the genome into 6 bp windows and calculate the 6 mer frequencies. Scanning chr6 of hg19: NNNNNN: 3719950 aaaaaa: 373380 tttttt: 372667 TTTTTT: 184768 AAAAAA: 182652 aaaaat: 143055 attttt: 142671 ATTTTT: 133646 TTTAAA: 133284 AAAAAT: 133130 TATTTT: 130672 AAAATA: 129572 TTTTAA: 129570 TTAAAA: 129177 aaaata: 123528 tatttt: 123134 atatat: 119872 …
Updated on 2013 November 5th to include mapping of piRNAs I still use blat as my multi-purpose alignment tool despite it being developed over 10 years ago. For those needing a simple introduction to blat, see my using blat post. Now I was wondering if blat could aligned short RNAs; the definition of short RNAs…
CpG islands are genomic regions that have a high frequency of cytosine nucleotides that occurs next to a guanine nucleotide. Download a CpG island BED file for hg19 from the UCSC Table Browser. For the Group, select “Regulation”, the track “CpG Islands” and output format = BED. According to the table schema, there are 28,691…