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=====Map v2 trimmed reads with Local alignment===== *Best mapping rate so far, I guess local alignment helps with all the sequencing errors in the reads? **Overall alignment rate comparable to V4 in vitro capture alignment rate **High multiple alignments but algorithm should choose the best mapping score *'''USING THIS SAM FILE FOR FURTHER ANALYSIS''' bowtie2 --local --phred33 -x CA12k_Nov2014_V7_H1H2 -q MC-20150121_CA12kNov2014_V7gDNA-4.R1.trimmedv2.fastq > CA12kNov2014_V7gDNA_R1_H1H2_localv2.sam 2> CA12kNov2014_V7gDNA_stderr_localv2.txt & 2390629 reads; of these: 2390629 (100.00%) were unpaired; of these: 76473 (3.20%) aligned 0 times 886116 (37.07%) aligned exactly 1 time 1428040 (59.73%) aligned >1 times 96.80% overall alignment rate bowtie2 --local --phred33 -x CA12k_Nov2014_V7_H1H2 -q MC-20150121_CA12kNov2014_V7cDNA-5.R1.trimmedv2.fastq > CA12kNov2014_V7cDNA_R1_H1H2_localv2.sam 2> CA12kNov2014_V7cDNA_stderr_localv2.txt & 3675652 reads; of these: 3675652 (100.00%) were unpaired; of these: 109047 (2.97%) aligned 0 times 1368908 (37.24%) aligned exactly 1 time 2197697 (59.79%) aligned >1 times 97.03% overall alignment rate samtools view -bS CA12kNov2014_V7gDNA_R1_H1H2_localv2.sam | samtools sort - CA12kNov2014_V7gDNA_R1_H1H2_sorted samtools view -h -F 4 CA12kNov2014_V7gDNA_R1_H1H2_sorted.bam > CA12kNov2014_V7gDNA_R1_H1H2_sorted_filtered.sam samtools view -bS CA12kNov2014_V7cDNA_R1_H1H2_localv2.sam | samtools sort - CA12kNov2014_V7cDNA_R1_H1H2_sorted samtools view -h -F 4 CA12kNov2014_V7cDNA_R1_H1H2_sorted.bam > CA12kNov2014_V7cDNA_R1_H1H2_sorted_filtered.sam *Using local alignment for quality trimmed reads leads to too many multiple alignments bowtie2 --local --phred33 -x CA12k_Nov2014_V7_H1H2 -q MC-20150121_CA12kNov2014_V7cDNA-5.R1.trimmed.fastq > CA12kNov2014_V7cDNA_R1_H1H2_local.sam 2> CA12kNov2014_V7cDNA_stderr_local.txt & 3675504 reads; of these: 3675504 (100.00%) were unpaired; of these: 11255 (0.31%) aligned 0 times 64099 (1.74%) aligned exactly 1 time 3600150 (97.95%) aligned >1 times 99.69% overall alignment rate
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