Mai 7, 2012

Illumina sequences indexed library IX0301 and IX0302

Data for this run is available here:

ftp://ftp.bcgsc.ca/supplementary/CP20120507/

To extract the archive, run:

1. gunzip *.tar.gz
2. tar -xvf *.tar

This directory contains:
transcriptome.tar.gz
microbes.tar.gz
./sequences

the result of running the microbe detection pipeline, as presented in: 
Moore RA, Warren RL, Freeman JD, Gustavsen JA, Chénard C, et al. (2011) The Sensitivity of Massively Parallel Sequencing for Detecting Candidate Infectious Agents Associated with Human Tissue. PLoS ONE 6(5): e19838. doi:10.1371/journal.pone.0019838 
is located in:
the "microbes" and "transcriptome" gziped folders, #read pair counts have been tallied for each samples belonging to library IX0301, IX0302 and both indexed libraries combined.

At the root of these directories is a side by side pair count comparison for all libraries combined:
e.g. microbes_paircount_all-IX030X-samples_accessions_SideBySide.csv
signifies:
microbes: result of microbial detection by paired-end sequence alignments.
all-IX030X0samples: indicate that all 5 libraries (CP027,CP028,CP030,CP031,CP036) were compared.
accessions/genus/species: indicate that the comparison was done at the accession,genus or species level, respectively
normalized: indicate that the pair count has been normalized based on the number of raw read pairs sequenced for each sample.

The IX0301 and IX0302 sub directories contain files for library comparison within each multiplexed library (ie. IX0301= CP027,CP028,CP030 and IX0302=CP031,CP036).  In addition, you may find the original .sam alignment file (microbes only) and a detailed report for each library (eg. qc-x_novo_vs_patho.sam-accession-CP027-single.csv)

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Using illumina barcode sequences corresponding to one of 5 CP sample library, paired-end reads were binned in the corresponding fastq files and located in the "sequences" folder.

Reads of a given pair are found in the
*.1.fq
*.2.fq
files.