Matt:LabNotes/2017-1-3: Difference between revisions

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>Mzcai
(Created page with "=CA12k_Oct2016_V4 in vitro Capture Sequencing Analysis== * For reference doing analysis *[[Matt:LabNotes/2016-11-15 | in vitro capture experiment]...")
 
>Mzcai
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===Check Sequencing Quality===
===Check Sequencing Quality===
*Currently in genomeMiner:~/scratch/CA12kOct2016_V4_CaptureAnalysis/Matt
   /media/Home_Raid1/kunzhang/softwares/fastx_toolkit-0.0.13.2/src/fastx_quality_stats/fastx_quality_stats -Q33 -i Index1_S1_L001_R1_001.fastq -o MC20161215_CA12kOct20161215_V4_T4_Indx1_qualstats.txt
   /media/Home_Raid1/kunzhang/softwares/fastx_toolkit-0.0.13.2/src/fastx_quality_stats/fastx_quality_stats -Q33 -i Index1_S1_L001_R1_001.fastq -o MC20161215_CA12kOct20161215_V4_T4_Indx1_qualstats.txt
   /media/Home_Raid1/kunzhang/softwares/fastx_toolkit-0.0.13.2/src/fastx_quality_stats/fastx_quality_stats -Q33 -i Index2_S2_L001_R1_001.fastq -o MC20161215_CA12kOct20161215_V4_SplintR_Indx2_qualstats.txt
   /media/Home_Raid1/kunzhang/softwares/fastx_toolkit-0.0.13.2/src/fastx_quality_stats/fastx_quality_stats -Q33 -i Index2_S2_L001_R1_001.fastq -o MC20161215_CA12kOct20161215_V4_SplintR_Indx2_qualstats.txt
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===Mapping Reads to Probelist===
===Mapping Reads to Probelist===
====Convert Probelist to Fasta File====
====Convert Probelist to Fasta File====
*In Dropbox\GradZhangLab\CA12k_Oct2016\HumanBrain_V4\invitroCapture
*Probelist: [[Media:padlockFile_0gap_HumanBrain_V4.txt]]  
*Probelist: [[Media:padlockFile_0gap_HumanBrain_V4.txt]]  
**[[Media:CA12kOct2016V4_Probelist2Fasta.txt | CA12kOct2016V4_Probelist2Fasta.pl]] to generate ref file: CA12k_Oct2016_V4_H1H2.fa
**[[Media:CA12kOct2016V4_Probelist2Fasta.txt | CA12kOct2016V4_Probelist2Fasta.pl]] to generate ref file: CA12k_Oct2016_V4_H1H2.fa

Revision as of 22:17, 6 January 2017

CA12k_Oct2016_V4 in vitro Capture Sequencing Analysis=

Check Sequencing Quality

  • Currently in genomeMiner:~/scratch/CA12kOct2016_V4_CaptureAnalysis/Matt
 /media/Home_Raid1/kunzhang/softwares/fastx_toolkit-0.0.13.2/src/fastx_quality_stats/fastx_quality_stats -Q33 -i Index1_S1_L001_R1_001.fastq -o MC20161215_CA12kOct20161215_V4_T4_Indx1_qualstats.txt
 /media/Home_Raid1/kunzhang/softwares/fastx_toolkit-0.0.13.2/src/fastx_quality_stats/fastx_quality_stats -Q33 -i Index2_S2_L001_R1_001.fastq -o MC20161215_CA12kOct20161215_V4_SplintR_Indx2_qualstats.txt
 /media/Home_Raid1/kunzhang/softwares/fastx_toolkit-0.0.13.2/src/fastx_quality_stats/fastx_quality_stats -Q33 -i Index3_S3_L001_R1_001.fastq -o MC20161215_CA12kOct20161215_V4_Amp_Indx3_qualstats.txt
 /media/Home_Raid1/kunzhang/softwares/fastx_toolkit-0.0.13.2/scripts/fastq_quality_boxplot_graph.sh -i MC20161215_CA12kOct20161215_V4_T4_Indx1_qualstats.txt -o MC20161215_CA12kOct20161215_V4_T4_Indx1_qualstats.png -t CA12kOct2016_V4_T4
 /media/Home_Raid1/kunzhang/softwares/fastx_toolkit-0.0.13.2/scripts/fastq_quality_boxplot_graph.sh -i MC20161215_CA12kOct20161215_V4_SplintR_Indx2_qualstats.txt -o MC20161215_CA12kOct20161215_V4_SplintR_Indx2_qualstats.png -t CA12kOct2016_V4_SplintR
 /media/Home_Raid1/kunzhang/softwares/fastx_toolkit-0.0.13.2/scripts/fastq_quality_boxplot_graph.sh -i MC20161215_CA12kOct20161215_V4_Amp_Indx3_qualstats.txt -o MC20161215_CA12kOct20161215_V4_Amp_Indx3_qualstats.png -t CA12kOct2016_V4_Ampligase

File:MC20161215 CA12kOct20161215 V4 T4 Indx1 qualstats.png File:MC20161215 CA12kOct20161215 V4 SplintR Indx2 qualstats.png File:MC20161215 CA12kOct20161215 V4 Amp Indx3 qualstats.png

  • Acceptable quality scores up to 65bp read, after 65bp quality drops

Mapping Reads to Probelist

Convert Probelist to Fasta File