Matt:LabNotes/2015-4-13
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Sequenced Rolony Analysis
- Library prep: Matt:LabNotes/2015-3-31
- Sequences are from CA12kNov2014_V4 Rolonies in BA8 tissue
- Raw data: /home/kunzhang/seqStore/150411_MiSeq/MC-SeqRolony_BA8V4_Mar3115-13_CCATGA_L001_R1_001.fastq
- Working directory:
- Genome-miner: BA8_V4_RolonySequencing -> /media/LTS_15T/MC_LTS/InSitu_MiSeq_150411_Analysis/
- Local: C:\Users\Matt\Dropbox\GradZhangLab\CA12k_Nov2014\SeqRolony
Mapping to Probelist
- Base quality
/home/kunzhang/softwares/fastx_toolkit-0.0.13.2/src/fastx_quality_stats/fastx_quality_stats -Q33 -i MC-SeqRolony_BA8V4_Mar3115-13_CCATGA_L001_R1_001.fastq -o MC-SeqRolony_BA8V4_Mar3115-13_CCATGA_L001_R1_qualstats.txt /home/kunzhang/softwares/fastx_toolkit-0.0.13.2/scripts/fastq_quality_boxplot_graph.sh -i MC-SeqRolony_BA8V4_Mar3115-13_CCATGA_L001_R1_qualstats.txt -o MC-SeqRolony_BA8V4_Mar3115-13_CCATGA_L001_R1_qualstats.png -t SequenceRolony_BA8_V4
File:MC-SeqRolony BA8V4 Mar3115-13 CCATGA L001 R1 qualstats.png
bowtie2-build CA12k_Nov2014_V4_H1H2.fa CA12k_Nov2014_V4_H1H2
bowtie2 --phred33 -x CA12k_Nov2014_V4_H1H2 -q MC-SeqRolony_BA8V4_Mar3115-13_CCATGA_L001_R1_001.fastq > SeqRolony_BA8V4.sam 2> SeqRolony_BA8V4_stderr.txt & 351727 reads; of these: 351727 (100.00%) were unpaired; of these: 16931 (4.81%) aligned 0 times 334796 (95.19%) aligned exactly 1 time 0 (0.00%) aligned >1 times 95.19% overall alignment rate
samtools view -bS SeqRolony_BA8V4.sam | samtools sort - SeqRolony_BA8V4_sorted samtools view -h -F 4 SeqRolony_BA8V4_sorted.bam > SeqRolony_BA8V4_sorted_filtered.sam
Count Probes and Genes
- SeqRolony_BA8V4_Genecounts.txt
- SeqRolony_BA8V4_Probecounts.txt