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=HiC Data Analysis ([[Daniel:Notebook/Haplotyping/2014-1-22|Started 1/22/2014]])= [[Daniel:Notebook/Haplotyping|Back to Calendar]] ==Novoalign== Indexed the reads using the data from [http://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp132Mask/ UCSC Genome Browser]. This download has the IUPAC codes already established, replacing variants with accepted non-ACTG codes. (Ex: If a base can be C or G, it is replaced by S) '''Create Index from downloaded UCSC genome data''' novoindex hg19_maskedSNP.nix *.fa '''Cell Sample 1, Lane 3, R1''' novoalign -d hg19_maskedSNP.nix -f /home/kunzhang/seqStore/140110_HiC_BingRen/PGP1_1-12.lane3.R1.fastq -# 1M -o SAM > PGP1_1-12.lane3.R1.1Mreads.sam # Hash length: 14 # Step size: 2 # Read Sequences: 945473 # Aligned: 795698 # Unique Alignment: 762170 # Gapped Alignment: 84930 # Quality Filter: 12048 # Illumina Q.Filter: 54527 # Homopolymer Filter: 449 # Elapsed Time: 2076.014 (sec.) # CPU Time: 34.3 (min.) # Done at Thu Jan 23 10:31:55 2014 '''Cell Sample 1, Lane 3, R2''' novoalign -d hg19_maskedSNP.nix -f /home/kunzhang/seqStore/140110_HiC_BingRen/PGP1_1-12.lane3.R2.fastq -# 1M -o SAM > PGP1_1-12.lane3.R2.1Mreads.sam # Hash length: 14 # Step size: 2 # Read Sequences: 945473 # Aligned: 795698 # Unique Alignment: 762170 # Gapped Alignment: 84930 # Quality Filter: 12048 # Illumina Q.Filter: 54527 # Homopolymer Filter: 449 # Elapsed Time: 2076.014 (sec.) # CPU Time: 34.3 (min.) # Done at Thu Jan 23 10:31:55 2014 ==Novoalign with Iterative Reads== The NBT paper from Bing Ren's lab says that they aligned the HiC data iteratively, trimming bases by 5 bp until the reads were no smaller than 25 bp if reads could not be placed initially. This is achieved using the -s (trimming) and -l (max length of trimmed read) flags. '''Cell Sample 1, Lane 3, R1; Iterative''' novoalign -d hg19_maskedSNP.nix -f /home/kunzhang/seqStore/140110_HiC_BingRen/PGP1_1-12.lane3.R1.fastq -# 1M -o SAM -s 5 -l 25 > PGP1_1-12.lane3.R1.1Mreads_it.sam & # Read Sequences: 945473 # Aligned: 932192 # Unique Alignment: 887771 # Gapped Alignment: 186486 # Quality Filter: 676 # Illumina Q.Filter: 54527 # Homopolymer Filter: 211 # Elapsed Time: 100111.344 (sec.) # CPU Time: 400.0 (min.) # Done at Fri Jan 24 19:48:00 2014
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