Matt:LabNotes/2015-3-19
CA12k_Nov2014_V4 in vitro Capture Sequencing Analysis
CA12kNov2014_Probelist2Fasta.pl
bowtie2-build CA12k_Nov2014_V4_H1H2.fa CA12k_Nov2014_V4_H1H2
bowtie2 --phred33 -x CA12k_Nov2014_V4_H1H2 -q MC-20150121_CA12kNov2014_V4gDNA-1.R1.fastq > CA12kNov2014_V4gDNA_R1_H1H2.sam 2> CA12kNov2014_V4gDNA_stderr.txt & 2573875 reads; of these:
2573875 (100.00%) were unpaired; of these: 115745 (4.50%) aligned 0 times 2458058 (95.50%) aligned exactly 1 time 72 (0.00%) aligned >1 times
95.50% overall alignment rate bowtie2 --phred33 -x CA12k_Nov2014_V4_H1H2 -q MC-20150121_CA12kNov2014_V4cDNA-2.R1.fastq > CA12kNov2014_V4cDNA_R1_H1H2.sam 2> CA12kNov2014_V4cDNA_stderr.txt & 2425688 reads; of these:
2425688 (100.00%) were unpaired; of these: 110744 (4.57%) aligned 0 times 2314903 (95.43%) aligned exactly 1 time 41 (0.00%) aligned >1 times
95.43% overall alignment rate
samtools view -bS CA12kNov2014_V4gDNA_R1_H1H2.sam | samtools sort - CA12kNov2014_V4gDNA_R1_H1H2_sorted samtools view -h -F 4 CA12kNov2014_V4gDNA_R1_H1H2_sorted.bam > CA12kNov2014_V4gDNA_R1_H1H2_sorted_filtered.sam
samtools view -bS CA12kNov2014_V4cDNA_R1_H1H2.sam | samtools sort - CA12kNov2014_V4cDNA_R1_H1H2_sorted samtools view -h -F 4 CA12kNov2014_V4cDNA_R1_H1H2_sorted.bam > CA12kNov2014_V4cDNA_R1_H1H2_sorted_filtered.sam