Difference between revisions of "2017 May Taeyoung Lab note"

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(BEASTgene)
 
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==Novel seq==
 
==Novel seq==
 
1. Align using mrFast
 
1. Align using mrFast
 +
 
2. assemble unmapped read using AbySS
 
2. assemble unmapped read using AbySS
 +
 
3. running novelseq
 
3. running novelseq
 +
 
  /alima9002/program/novelseq-upload$ ./novel_cluster /alima9002/novelseq/raw CS-12.W82.mrfast.OEA.all.sam Gmax.275.sat.parsed /alima9002/novelseq/raw/chr /alima9002/novelseq/raw/CS-12.fastq.trimmed /alima9002/novelseq/raw/CS-12.W82.mrfast.out.all.ins.size 100000000
 
  /alima9002/program/novelseq-upload$ ./novel_cluster /alima9002/novelseq/raw CS-12.W82.mrfast.OEA.all.sam Gmax.275.sat.parsed /alima9002/novelseq/raw/chr /alima9002/novelseq/raw/CS-12.fastq.trimmed /alima9002/novelseq/raw/CS-12.W82.mrfast.out.all.ins.size 100000000
 +
 +
==5.29==
 +
===BEASTgene===
 +
/data2/alima90/program/BEASTGen/bin/beastgen template_JTT_G.xml 11.10.fa.nexus > 11.10.fa.xml

Latest revision as of 05:16, 27 June 2017

Novel seq

1. Align using mrFast

2. assemble unmapped read using AbySS

3. running novelseq

/alima9002/program/novelseq-upload$ ./novel_cluster /alima9002/novelseq/raw CS-12.W82.mrfast.OEA.all.sam Gmax.275.sat.parsed /alima9002/novelseq/raw/chr /alima9002/novelseq/raw/CS-12.fastq.trimmed /alima9002/novelseq/raw/CS-12.W82.mrfast.out.all.ins.size 100000000

5.29

BEASTgene

/data2/alima90/program/BEASTGen/bin/beastgen template_JTT_G.xml 11.10.fa.nexus > 11.10.fa.xml