Tag Archives: genome

bowtie and multimapping reads

Posted on November 26, 2011 by Davo

I first tried this with BWA. Now I’ll try it with bowtie. Consider this reference sequence: >artificial ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG and this read: … Continue reading →

Posted in bioinformatics | Tagged , , | Leave a comment

bwa and multi mapping reads

Posted on October 11, 2011 by Davo

Consider this reference sequence: >artificial ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG and this read: >tag ACGTACGTACGTACGTAGGTACGTA Using bwa (Program: bwa (alignment via Burrows-Wheeler transformation) Version: 0.5.9-r1) this is the SAM output tag 0 artificial 57 0 25M * 0 0 ACGTACGTACGTACGTAGGTACGTA … Continue reading →

Posted in bioinformatics | Tagged , , | Leave a comment

Perl and SAM

Posted on January 28, 2011 by Davo

Lincoln Stein has written a bunch of modules to deal with SAM/BAM files. Check out the CPAN module. To install the Perl module on a machine where you don’t have root access, follow these instructions. Using this module, I recreated … Continue reading →

Posted in bioinformatics, programming | Tagged , , , | 4 Comments

Genome scan for 6mer frequency

Posted on November 26, 2010 by Davo

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: … Continue reading →

Posted in bioinformatics, programming | Tagged , , | Leave a comment

Can we use blat to map miRNA’s?

Posted on November 16, 2010 by Davo

From miRBase downloaded the mature miRNA’s. In the file, there are currently 1,223 miRNA’s for the human genome. Using default blat settings, 152 (133 map to only one loci) of the mature human miRNA’s can be mapped to the assembled … Continue reading →

Posted in bioinformatics | Tagged , , | Leave a comment