Gene list from copy number variation data
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7.3 years ago
akij ▴ 190

I have a list of copy number variation data I got from TCGA website. The data looks like this

Sample  Chromosome  Start   End Num_Probes  Segment_Mean
AMAZE_p_TCGASNP_b86_87_88_N_GenomeWideSNP_6_C08_735516  1   61735   12785720    6509    0.0628
AMAZE_p_TCGASNP_b86_87_88_N_GenomeWideSNP_6_C08_735516  1   12792599    13278863    57  -0.5061
AMAZE_p_TCGASNP_b86_87_88_N_GenomeWideSNP_6_C08_735516  1   13326062    25256850    7563    0.0667
AMAZE_p_TCGASNP_b86_87_88_N_GenomeWideSNP_6_C08_735516  1   25266637    25336819    32  0.6428
AMAZE_p_TCGASNP_b86_87_88_N_GenomeWideSNP_6_C08_735516  1   25336853    57755402    18550   0.0636
AMAZE_p_TCGASNP_b86_87_88_N_GenomeWideSNP_6_C08_735516  1   57757884    69368291    8418    0.1007
AMAZE_p_TCGASNP_b86_87_88_N_GenomeWideSNP_6_C08_735516  1   69375800    84595696    9774    0.0659

I want to get the list of genes within each regions start and end. How can I easily do this? Thanks in advance.

CNV gene • 1.1k views
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Extract coordinates and Intersect with a gtf file with known genes.

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