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
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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