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Moderní metody analýzy genomu - analýza Mgr. Nikola Tom Brno, 2.4.2014

Modern í metody analýzy genomu - anal ýza

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Modern í metody analýzy genomu - anal ýza. Mgr. Nikola Tom. Brn o , 2.4 .201 4. Workflow. Raw sequence = fastq. Biological sequence Corresponding quality scores ASCII character ( fasta + qual , csfasta + csqual , sff ) @ - PowerPoint PPT Presentation

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Page 1: Modern í metody analýzy genomu -  anal ýza

Moderní metody analýzy genomu- analýza

Mgr. Nikola Tom

Brno, 2.4.2014

Page 2: Modern í metody analýzy genomu -  anal ýza

Workflow

Page 3: Modern í metody analýzy genomu -  anal ýza

Raw sequence = fastq

• Biological sequence• Corresponding quality scores• ASCII character• (fasta+ qual, csfasta + csqual, sff)

@SEQ_ID GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT + !''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65

Page 4: Modern í metody analýzy genomu -  anal ýza

FastQC

Page 5: Modern í metody analýzy genomu -  anal ýza

Cutadapt

• Adaptor trimming (miRNA)• Quality filtering• Length filtering

Page 6: Modern í metody analýzy genomu -  anal ýza
Page 7: Modern í metody analýzy genomu -  anal ýza

Read mapping => SAM, BAM

• Usually mapping reads on reference• miRNA - special case– Grouping and annotate against mirBase

• DNA– BWA, Bowtie, Bfast, SHRiMPclc

• RNA– TopHat (de novo splice aligner)

• Commercial– CLC Genomics Workbench

Page 8: Modern í metody analýzy genomu -  anal ýza

SAM

Page 9: Modern í metody analýzy genomu -  anal ýza

Alignment

Page 10: Modern í metody analýzy genomu -  anal ýza

Mapping, Coverage reports

• Important checkout for lab protocol• Specificity of PCR• Normalization• Settings of variant calling threshold, CNV

Page 11: Modern í metody analýzy genomu -  anal ýza
Page 12: Modern í metody analýzy genomu -  anal ýza

SNV and small InDel Calling

• Coverage• Frequency• Base quality

• !!!• Genomic context (homopolymers)• Nucleotide type• Position in read (errors at the read end)• Alignment errors

Page 13: Modern í metody analýzy genomu -  anal ýza

CNV variations

Page 14: Modern í metody analýzy genomu -  anal ýza

Structural variations

• Mate-pair library• Long InDel• Translocation

Page 15: Modern í metody analýzy genomu -  anal ýza
Page 16: Modern í metody analýzy genomu -  anal ýza

Annotating and filtering

• Gene • Transcript• dbSNP• Regulation• Comparative genomics• Repeats• Functional • Gene ontology• miRNA targets• Etc.