medp_pilpe-20110620
-------------------

stats.txt:  Summary  statistics  associated  with contigs.fa. In-
cludes the total number of sequences and bases in the contig set,
N50,  etc.   Q1,  Q2, Q3 are the quartiles of the reported contig
lengths. B1000 and B1000 indicate the  percentage  of  bases  in-
volved in contigs at least 1000 bp and 2000 bp, respectively.

--

contigs.fa:  Contigs from the assembly, min. 100 bp. Possibly in-
cludes UTRs. Sequences may contain IUPAC ambiguity  codes  repre-
senting  ambiguous  bases,  http://www.bioinformatics.org/sms/iu-
pac.html.

--

peptides.fa: Protein products predicted by ESTScan, min.  30  aa.
These  do  not  necessarily  include initial methionine. Sequence
identifiers for these predicted products correspond to the  asso-
ciated nucleotide sequence in contig.fa, and are provided suffix-
es #1, #2, etc., to accommodate multiple predictions.

--

readcounts/*.dat: Read counts obtained by post hoc  alignment  of
reads  using  BWA 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.;  con-
tig_id     is     the    contig    identifier,    for    example,
medp_pilpe-20110620|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.

                        ***PLEASE NOTE***
Read counts are provided for quality assessment of the contig set
only.  For  differential  expression  analyses, it is recommended
more sophisticated estimators of relative expression level be em-
ployed.

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National Center for Genome Resources
http://www.ncgr.org