Ns126:Calendar/NOTES/2016-1-5: Difference between revisions
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>Shicheng |
>Shicheng |
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*Fastq donwload address: [[File:Haib.download.files.txt]] | *Fastq donwload address: [[File:Haib.download.files.txt]] | ||
xargs -n 1 curl -O -L < haib.download.files.txt | xargs -n 1 curl -O -L < haib.download.files.txt | ||
===Check Phred Score=== | |||
perl ~/bin/checkphred.pl *fastq | |||
===Fastq Quality Control=== | ===Fastq Quality Control=== |
Revision as of 08:54, 7 January 2016
Collection RRBS Dataset From Richard Myers, HAIB (Encode Project)
Data Description
Fastq Download
- Fastq donwload address: File:Haib.download.files.txt
xargs -n 1 curl -O -L < haib.download.files.txt
Check Phred Score
perl ~/bin/checkphred.pl *fastq
Fastq Quality Control
trim_galore --phred64 --fastqc --illumina --non_directional --rrbs *.fastq
Fastq Alignment
bismark --bowtie2 --phred64-quals --fastq -L 30 -N 1 /home/shg047/db/aligndb/hg19/bismark -1 ENCFF000LUN.fastq_qual_trimmed.fastq -o ../bam