Hi,

I tried to find suitable R/BioC packages to analyze chip-seq data (Illumina
GA) starting with raw seq files with quality score, and the ELAND alignment
files (result and sorted formats). I followed notes and examples from BioC
workshops (2008-2010), used chipseq etc to input data. However, the R
stopped reading data when I imported single eland result file (about 1GB). I
am wondering if anyone in this list could help me in pointing at the right
packages or tools for the following questions:

1. import raw seq files with quality score
2. use multiple CPU
3. alignment using human or custom genome, how to create custom genome
4. make WIG or BED files to upload to UCSC genome browser
5. transcription factor analysis

Thanks,

Tiandao

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