Matt:LabNotes/2015-3-19: Difference between revisions
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>Mzcai (Created page with "==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 ...") |
>Mzcai mNo edit summary |
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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 & | 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 reads; of these: | ||
2573875 (100.00%) were unpaired; of these: | 2573875 (100.00%) were unpaired; of these: | ||
115745 (4.50%) aligned 0 times | 115745 (4.50%) aligned 0 times | ||
2458058 (95.50%) aligned exactly 1 time | 2458058 (95.50%) aligned exactly 1 time | ||
72 (0.00%) aligned >1 times | 72 (0.00%) aligned >1 times | ||
95.50% overall alignment rate | 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 & | 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 reads; of these: | ||
2425688 (100.00%) were unpaired; of these: | 2425688 (100.00%) were unpaired; of these: | ||
110744 (4.57%) aligned 0 times | 110744 (4.57%) aligned 0 times | ||
2314903 (95.43%) aligned exactly 1 time | 2314903 (95.43%) aligned exactly 1 time | ||
41 (0.00%) aligned >1 times | 41 (0.00%) aligned >1 times | ||
95.43% overall alignment rate | 95.43% overall alignment rate | ||
samtools view -bS CA12kNov2014_V4gDNA_R1_H1H2.sam | samtools sort - CA12kNov2014_V4gDNA_R1_H1H2_sorted | 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 -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 -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 | samtools view -h -F 4 CA12kNov2014_V4cDNA_R1_H1H2_sorted.bam > CA12kNov2014_V4cDNA_R1_H1H2_sorted_filtered.sam |
Revision as of 01:54, 20 March 2015
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