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README by S. Singhal 
sonal.singhal1@gmail.com
16 June 2011
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This tarball consists of three main types of files.

1. library*.sorted.bam => These are the files that resulted from using Bowtie to map the trimmed reads in the seq/ dir to the the RGSC3.4 assembly. Also included are associated index (*.bai) files
2. assembleMito.fa => This is the assembly of the sequenced rat's mitochondrial genome resulting from de novo assembly of the reads using ABySS.
3. seq/ contains the reads trimmed for contamination, adapter, and low-quality as discussed in the publication. library5* is derived from the molar. library6* is derived from the toe. *_1_* reads are forward reads; *_2_* reads are reverse reads. Any reads that lost their mate-pair during the trimming process are not included here although they were used for mapping. These reads are available from S. Singhal upon request.


Note: scripts used for analysis and other data are available from S. Singhal upon request.