Kun:LabNotes/MONOD/2014-8-27

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Target selection for NimbleGen SeqCap EPI Choice[edit]

  • Dinh's UMRs cover over 40Mb. In order to fit in the 30Mb limit of NimbleGen's array, I first removed all repetitive regions from the UMRs.
 /home/kunzhang/softwares/bedtools-2.17.0/bin/bedtools subtract  -a blood.UMRs.tab.txt -b hg19_rmsk_bed.txt > blood.UMRs.non-repetitive.bed
  • Then I merge with the LMS clusters
 cat blood.UMRs.non-repetitive.bed whole_blood_LMS_clusters_BED.txt | sort -k 1,1 -k 2,2n | /home/kunzhang/softwares/bedtools-2.17.0/bin/bedtools  merge -d 80 -i - > blood.UMRs.non-repetitive.blood_LMS_clusters.merged.bed.txt
  • To further reduce the total capture size, I extracted 29,936 regions that are autosomal and 100-2750bp. The total size is 28.4Mb.
  • For the regions larger than 2.75kb, I did the interection with the blood LMS clusters, and included the 3146 regions to the target list.
 /home/kunzhang/softwares/bedtools-2.17.0/bin/bedtools intersect  -a blood.UMRs.non-repetitive.blood_LMS_clusters_2.75kUp.merged.bed -b whole_blood_LMS_clusters_BED.txt > blood.UMRs.non-repetitive.blood_LMS_clusters_2.75kUp.merged.whole_blood_LMS_clusters.bed.txt