Issues

• CpG_preparation.R to check whether genome is hosted on UCSC before trying to pull down CpG islands

  clark-lab/Bisulfite_tools#31 · Filter by author astatham opened on Nov 12, 2013

• Add option for NOMe

  clark-lab/Bisulfite_tools#30 · Filter by author astatham opened on Oct 31, 2013

• Add lambda genome for % conversion

  enhancement
  clark-lab/Bisulfite_tools#29 · Filter by author astatham opened on Oct 14, 2013

• bedGraph_to_Rdata still uses hg19

  bug
  clark-lab/Bisulfite_tools#28 · Filter by author astatham opened on Oct 10, 2013

• Add (optional?) FLASh integration

  enhancement
  clark-lab/Bisulfite_tools#26 · Filter by author astatham opened on Aug 27, 2013

• Pipeline fails if the directory name starts with a number at the first qsub

  bug
  clark-lab/Bisulfite_tools#25 · Filter by author astatham opened on Aug 26, 2013

• Add option to trim sequenom adaptors (needed for MiSeq)

  enhancement
  clark-lab/Bisulfite_tools#24 · Filter by author astatham opened on Aug 26, 2013

• Integrate MiSeq amplicon alignment

  enhancement
  clark-lab/Bisulfite_tools#23 · Filter by author astatham opened on Aug 26, 2013
  1

• Split fastqc section into separate qsub

  bug
  clark-lab/Bisulfite_tools#21 · Filter by author astatham opened on Aug 10, 2013
  1

• Merge PE and SE scripts

  clark-lab/Bisulfite_tools#20 · Filter by author astatham opened on Aug 5, 2013

• Remove wolfpack specific gunk

  Code cleanupNot important
  clark-lab/Bisulfite_tools#19 · Filter by author astatham opened on Aug 1, 2013

• Add fastq_screen to prep_reads

  Not important
  clark-lab/Bisulfite_tools#18 · Filter by author astatham opened on Jul 26, 2013

• Execute all qsub scripts from the output/ directory

  Code cleanup
  clark-lab/Bisulfite_tools#16 · Filter by author astatham opened on Jul 24, 2013
  1

• Convert main script over to a Makefile - for free checkpointing

  enhancementWhat's the worst that could happen?
  clark-lab/Bisulfite_tools#14 · Filter by author astatham opened on Jul 23, 2013

• Create report at end of run

  enhancement
  clark-lab/Bisulfite_tools#10 · Filter by author astatham opened on Jul 16, 2013

• Improve logs

  enhancement
  clark-lab/Bisulfite_tools#7 · Filter by author astatham opened on Jul 16, 2013

• Allow any number of chunks (currently hardcoded at 20)

  Not important
  clark-lab/Bisulfite_tools#6 · Filter by author astatham opened on Jul 13, 2013