medp_colfo-20110601

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Q1, Q2, Q3 are the quartiles of the reported contig lengths. B1000 and
B1000 indicate the percentage of bases involved in contigs at least 1000
bp and 2000 bp, respectively.

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stats.txt: Summary statistics associated with contigs.fa. Includes
total number of sequences and bases in the contig set, N50, etc. See
note above on Q1, Q2, Q3, B1000, and B2000.

contigs.fa: Contigs from assembly, min. 100 bp. Possibly includes
UTRs. Sequences may contain IUPAC ambiguity codes representing ambiguous
bases, http://www.bioinformatics.org/sms/iupac.html.


peptides.fa: Protein products predicted by ESTScan. Does not necessarily
include initial methionine. Possibly more than one polypeptide per contig.

readcounts/*.dat: Read counts obtained by post hoc alignment of
reads to reported contigs, per sample, via gsnap with default
parameters. Tab-delimited columns with the format

 sample contig_id all_aligned unique_aligned paired_aligned contig_len

where sample indicates the sample, library, tissue, etc.; contig_id is the
contig identifier, for example, medp_colfo-20110601|1234); all_aligned is
the number of reads aligned to this contig; unique_aligned is the number
of reads that aligned uniquely to this contig; and paired_aligned is the
number of pairs aligned to this contig. Contig_len is the length of the
contig in bp.