Entering edit mode
7.3 years ago
akij
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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.
Extract coordinates and Intersect with a gtf file with known genes.