Hello Sir/Ma'am,
1] Trying to apply oncocnv for exome data i.e. without reference to amplicon id. What should be modification required in bed file for applying it on Exome data.
Standard bed file:
track name="4477685_CCP_Designed" description="Amplicon_Insert_4477685_CCP" type=bedDetail
chr1 2488068 2488201 AMPL242431688 0 TNFRSF14
Bed file used for Exome data:
track name="Covered" description="Illumina Exon - Genomic regions covered by probes" db=hg19
chr1 14694 14814 AMPL1354 0 WASH7P
Above bed file used, contains random amplicon id in 3rd column and 0 in 5th column, is it right strategy to use for Exon seq data?
2] While applying ONCOCNV for EXON data what precautions or prerequisite should be taken care of?
Kindly Guide.
Regards,
Vyomesh
Hello Sir/Ma'am,
1] Trying to apply oncocnv for exome data i.e. without reference to amplicon id. What should be modification required in bed file for applying it on Exome data.
Standard bed file:
track name="4477685_CCP_Designed" description="Amplicon_Insert_4477685_CCP" type=bedDetail
chr1 2488068 2488201 AMPL242431688 0 TNFRSF14
Bed file used for Exome data:
track name="Covered" description="Illumina Exon - Genomic regions covered by probes" db=hg19
chr1 14694 14814 AMPL1354 0 WASH7P
Above bed file used, contains random amplicon id in 3rd column and 0 in 5th column, is it right strategy to use for Exon seq data?
2] While applying ONCOCNV for EXON data what precautions or prerequisite should be taken care of?
Kindly Guide.
Regards,
Vyomesh