From Bioinformatics Core

These pages are meant to share our experience with various tools and topics related to bioinformatics. Don't expect formal documentation; the idea is that we'll post quickly here to share tips and "quick start" directions with each other, then gradually touch up these pages as we gain deeper experience with each topic.

There is already a detailed and active Wiki done by Brad at Bradbot Wiki

Data Analysis

Bioinformatics Core Pages / Tools:

• Bioshare File Structure
• Bioshare REST API
• SLIMS package
• Using the CMGI web interface for Administrators
• Using the CMGI web interface for Users
• Often used file locations

System Administration

"Workarounds":

• for *nix command line
• for bioinformatics tools
• convert Solexa realign files to UCSC BED format
• loop in bash
• running qsub on every node but one

perl scripts:

• count_fasta.pl .. obtain length histogram, GC-content, etc. for sequences in a fasta-format file (Brad Sickler)
• fasta1line.pl .. remove newlines to put all sequence on one line following header line, for all sequences in a fasta-format file (Joe Fass)
• trim_fasta.pl .. trim bases from beginning and/or ends of sequences and qualities in a fasta/q-format file (Joe Fass)
• subsequence.pl .. cut out a sub-sequence from sequences and qualities in a fasta/q-format file (Joe Fass)

Bioinformatics course:

• Basic Unix Commands
• Basic Cluster Computing Commands (Sun Grid Engine)
• Bioinformatics Course - sissrs.pl
  • Sissrs.pl options
• Bioinformatics Course - macs
  • MACS options
• Using BLAST on the cluster
  • BLAST options
• Using the Nano editor to edit scripts
• Assembly hands-on session starting point
• Using PuTTY
• Using WinSCP
• Loading a custom track into the UCSC Genome Browser