Dinh 2011/NOTES/2011-12-22: Difference between revisions
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Here is a nice diagram explaining this from SeqAnswers: | Here is a nice diagram explaining this from SeqAnswers: | ||
[[File:bwaTrimming.jpg | 100px]] | [[File:bwaTrimming.jpg | 100px]] | ||
basically, trim where the average read quality from 3' end gets below the -q cutoff. | |||
Thus I will use -q 20 for trimming. | Thus I will use -q 20 for trimming. | ||
* I will map all the fastq first using: | * I will map all the fastq first using: |
Latest revision as of 18:51, 23 December 2011
- 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