Dinh 2011/NOTES/2011-12-22

From ZhangLabWiki
Jump to navigation Jump to search
  • Installed my own 3TB hard drive on meangenemachine: dinh_hdd
  • Making it nfs mountable:
 Server:
 1) add new entry to /etc/exports
    /media/dinh_hdd genemapster.dynamic.ucsd.edu(ro,async)
 2) restart nfs
    /etc/init.d/nfs-kernel-server restart
 3) change permissions on dinh_hdd
    sudo chmod ugo+rwx 
 Client:
 1) restart nfs
    /etc/init.d/nfs-kernel-server restart
 2) mount
    sudo mount meangenemachine.dynamic.ucsd.edu:/media/dinh_hdd dinh-nfs/
 
  • Now I can map the data on genemapster and meangenemachine

Yi Zhang Lab (UNC) 24 ChIP/DIP Data[edit]

Analysis of enrichment in repeats[edit]

PE Data[edit]

  • FastqC on 100,000 reads
READ1 (Indx15)
File:YiZhang 24ChIP PE read1.png
READ2 (Indx2)
File:YiZhang 24ChIP PE read2.png
  • Trimming 5 bp from 5' of Read1 and 20 bp from 5' of Read2
  • Sequence size is 300-600 (Alan's gel cut labnote)
  • Mapping procedure from BWA's manual:
bwa aln ref.fa -b1 reads.bam > 1.sai 
bwa aln ref.fa -b2 reads.bam > 2.sai 
bwa sampe ref.fa 1.sai 2.sai reads.bam reads.bam > aln.sam
  • I expect that if the paired read flank onto repeats, one read will map uniquely while another will be mapped non-uniquely. BWA sampe will find the best unique mapping for the pair.
  • Trimming with BWA is most based on quality score, according to the manual,
-q is : Parameter for read trimming. BWA trims a read down to argmax_x{\sum_{i=x+1}^l(INT-q_i)} if q_l<INT where l is the original read length. [0]
Here is a nice diagram explaining this from SeqAnswers:
File:BwaTrimming.jpg
basically, trim where the average read quality from 3' end gets below the -q cutoff.
Thus I will use -q 20 for trimming.
  • I will map all the fastq first using:
bwa aln -l 28 -k 3 -t 16 -q 20 -I /media/disk-1/Dinh_Scratch/mm9Annotations-iGenomeUCSC/BWAIndex/mm9 
    • checked that quality values are in ASCII-64!
  • Ran mapping..
 15.7% of bases are trimmed for Read 1