Kun:LabNotes/MONOD/2014-8-12: Difference between revisions
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./[[Media:bed2Clusters.txt|bed2Clusters.pl]] MONOD_primary_tumor_RRBS_combined.sorted.BED.txt > [[Media:MONOD_primary_tumor_RRBS_targets.BED.txt|MONOD_primary_tumor_RRBS_targets.BED.txt]] | ./[[Media:bed2Clusters.txt|bed2Clusters.pl]] MONOD_primary_tumor_RRBS_combined.sorted.BED.txt > [[Media:MONOD_primary_tumor_RRBS_targets.BED.txt|MONOD_primary_tumor_RRBS_targets.BED.txt]] | ||
*A total of 198,439 regions in the autosomes, with a total size of 48.8Mb. | *A total of 198,439 regions in the autosomes, with a total size of 48.8Mb. | ||
===2. Check the total read depth for CpG sites within the RRBS targets=== | |||
cat 6-P-10.methylFreq | /home/dinh/scripts/methylFreq2BED.pl 1 | /home/kunzhang/softwares/bedtools-2.17.0/bin/bedtools intersect -wa -a - -b /home/kunzhang/CpgMIP/Data/MONOD/MONOD_primary_tumor_RRBS_targets.BED.txt | /home/kunzhang/CpgMIP/Data/MONOD/bed_total_RD.pl | |||
cat 6-P-10.methylFreq | /home/dinh/scripts/methylFreq2BED.pl 1 | /home/kunzhang/CpgMIP/Data/MONOD/bed_total_RD.pl | |||
On-target read depth Total CpG read depth % on-target | |||
6-P-10 15,965,319 20,663,932 77.3% | |||
6-P-1 10,145,982 13,357,081 76.0% | |||
6-T-1_1 42,122,819 51,404,477 81.9% | |||
6-T-2_1 39,727,871 47,770,689 83.2% | |||
CTT-frozen-100ng_1 50,274,814 55,387,277 90.8% | |||
CTT-frozen-5ng_1 14,303,236 15,310,475 93.4% |
Revision as of 00:11, 13 August 2014
RRBS data analysis (continued)
1. Compile a list of RRBS targets
- Take all the RRBS data that we generated from primary tumor samples, concatenate all the methylFreq files, and generate a single BED file.
cat 6-T-1_1.methylFreq 6-T-1_2.methylFreq 6-T-2_1.methylFreq 6-T-2_2.methylFreq 6-T-3_1.methylFreq 6-T-3_2.methylFreq 6-T-4_1.methylFreq 6-T-4_2.methylFreq 6-T-5_1.methylFreq 6-T-5_2.methylFreq 7-T-1_1.methylFreq 7-T-1_2.methylFreq 7-T-2_1.methylFreq 7-T-2_2.methylFreq 7-T-3_1.methylFreq 7-T-3_2.methylFreq 7-T-4_1.methylFreq 7-T-4_2.methylFreq 7-T-5_1.methylFreq 7-T-5_2.methylFreq CTT-FFPE-100ng_1.methylFreq CTT-FFPE-100ng_2.methylFreq CTT-FFPE-5ng_1.methylFreq CTT-FFPE-5ng_2.methylFreq CTT-frozen-100ng_1.methylFreq CTT-frozen-100ng_2.methylFreq CTT-frozen-5ng_1.methylFreq CTT-frozen-5ng_2.methylFreq PC-T-1_1.methylFreq PC-T-1_2.methylFreq PC-T-2_1.methylFreq PC-T-2_2.methylFreq PC-T-4_1.methylFreq PC-T-4_2.methylFreq PC-T-6_1.methylFreq PC-T-6_2.methylFreq PC-T-7_1.methylFreq PC-T-7_2.methylFreq | /home/dinh/scripts/methylFreq2BED.pl 20 > /home/kunzhang/CpgMIP/Data/MONOD/MONOD_primary_tumor_RRBS_combined.BED.txt
cat MONOD_primary_tumor_RRBS_combined.BED.txt | sort -k1,1 -k2,2n > MONOD_primary_tumor_RRBS_combined.sorted.BED.txt
- Group the sites covered into clusters:
./bed2Clusters.pl MONOD_primary_tumor_RRBS_combined.sorted.BED.txt > MONOD_primary_tumor_RRBS_targets.BED.txt
- A total of 198,439 regions in the autosomes, with a total size of 48.8Mb.
2. Check the total read depth for CpG sites within the RRBS targets
cat 6-P-10.methylFreq | /home/dinh/scripts/methylFreq2BED.pl 1 | /home/kunzhang/softwares/bedtools-2.17.0/bin/bedtools intersect -wa -a - -b /home/kunzhang/CpgMIP/Data/MONOD/MONOD_primary_tumor_RRBS_targets.BED.txt | /home/kunzhang/CpgMIP/Data/MONOD/bed_total_RD.pl cat 6-P-10.methylFreq | /home/dinh/scripts/methylFreq2BED.pl 1 | /home/kunzhang/CpgMIP/Data/MONOD/bed_total_RD.pl On-target read depth Total CpG read depth % on-target 6-P-10 15,965,319 20,663,932 77.3% 6-P-1 10,145,982 13,357,081 76.0% 6-T-1_1 42,122,819 51,404,477 81.9% 6-T-2_1 39,727,871 47,770,689 83.2% CTT-frozen-100ng_1 50,274,814 55,387,277 90.8% CTT-frozen-5ng_1 14,303,236 15,310,475 93.4%