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]...") |
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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=
- For reference doing analysis
- in vitro capture experiment
- Indx1: T4
- Indx2: SplintR
- Indx3: Ampligase
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
- In Dropbox\GradZhangLab\CA12k_Oct2016\HumanBrain_V4\invitroCapture
- Probelist: Media:padlockFile_0gap_HumanBrain_V4.txt
- CA12kOct2016V4_Probelist2Fasta.pl to generate ref file: CA12k_Oct2016_V4_H1H2.fa