BYe9.head.map contains aligned reads from an RNA-seq experiment.

This file gives some details on how BYe9.head.map was obtained.

Experimental data
-----------------

- Type of experiment: RNA-seq

- Organism: Yeast

- Strain: Lab strain (BY4716). The BY4716 strain is very close in sequence to
  the reference strain of Saccharomyces cerevisiae (S288C strain).

- Technology: Solexa (first version of the Illumina Genome Analyzer DNA
  sequencer).

- Length of the reads: 32 nucleotides.

- More information about the experiment at:
    http://genomics.princeton.edu/caudylab/yeast_cDNA_sequencing/

Alignment
---------

- Reference genome: was downloaded from
    ftp://ftp.yeastgenome.org/yeast/data_download/sequence/NCBI_genome_source/
  on Jan. 20 2010.
  This genome (we'll call it SGD20100120) is almost identical to sacCer2 from
  UCSC (both correspond to the S288C strain) except that:
    (a) SGD20100120 is more recent than sacCer2 (sacCer2 is a snapshot of the
        same folder but from June 2008).
    (b) Chromosome names are different:
          SGD20100120: chr01, chr02, ... chr16, chrmt
          sacCer2: chrI, chrII, ... chrXVI, chrM, 2micron
    (c) The 2-micron plasmid sequence is not included in SGD20100120.
    (d) The chromosome sequences are the same except for chr10 and chr14.
    (e) chr10 has 1 deletion compared to chrX (at position 126896, a T).
    (f) chr14 has 2 substitutions and 1 insertion compared to chrXIV (they
        all occur between pos 472581 and 472585).
  
- Aligner: Bowtie 0.12.1

  Command used: bowtie -t -p 4 S288C BYe9.fastq.txt BYe9.map
  Output:
    Time loading forward index: 00:00:00
    Time loading mirror index: 00:00:01
    Seeded quality full-index search: 00:00:35
    # reads processed: 5225331
    # reads with at least one reported alignment: 4927080 (94.29%)
    # reads that failed to align: 298251 (5.71%)
    Reported 4927080 alignments to 1 output stream(s)
    Time searching: 00:00:40
    Overall time: 00:00:40

  More info on Bowtie at: http://bowtie-bio.sourceforge.net/manual.shtml

Extraction of the first million alignments
------------------------------------------

- BYe9.head.map was obtained by extracting the first million of lines
  from BYe9.map. Command used: head -n 1000000 BYe9.map > BYe9.head.map

