Matt:LabNotes/2015-4-27: Difference between revisions
Jump to navigation
Jump to search
>Mzcai |
>Mzcai mNo edit summary |
||
Line 20: | Line 20: | ||
*RNA-Seq data from: /media/LTS_33T/RL_LTS33T/201404_201405_7Samples_BulkNucleiBatch1-20140623_Expt146/STAR$ | *RNA-Seq data from: /media/LTS_33T/RL_LTS33T/201404_201405_7Samples_BulkNucleiBatch1-20140623_Expt146/STAR$ | ||
**RL-BA8-sec9-t-N701-15May14_S1_mapped/RL-BA8-sec9-t-N701-15May14_S1_Aligned.sorted.bam | **RL-BA8-sec9-t-N701-15May14_S1_mapped/RL-BA8-sec9-t-N701-15May14_S1_Aligned.sorted.bam | ||
***59,038,666 reads | |||
**RL-BA8-sec9-n-N702-15May14_S2_mapped/RL-BA8-sec9-n-N702-15May14_S2_Aligned.sorted.bam | **RL-BA8-sec9-n-N702-15May14_S2_mapped/RL-BA8-sec9-n-N702-15May14_S2_Aligned.sorted.bam | ||
***45,222,268 reads | |||
*Commands | |||
<!-- | |||
/home/mzcai/softwares/bedtools-2.20.1/bin/coverageBed -hist -abam /media/LTS_33T/RL_LTS33T/201404_201405_7Samples_BulkNucleiBatch1-20140623_Expt146/STAR/RL-BA8-sec9-t-N701-15May14_S1_mapped/RL-BA8-sec9-t-N701-15May14_S1_Aligned.sorted.bam -b CA12k_Nov2014_V4_hg19.bed > coverage.hist.BA8-t.V4.txt & | |||
/home/mzcai/softwares/bedtools-2.20.1/bin/coverageBed -hist -abam /media/LTS_33T/RL_LTS33T/201404_201405_7Samples_BulkNucleiBatch1-20140623_Expt146/STAR/RL-BA8-sec9-n-N702-15May14_S2_mapped/RL-BA8-sec9-n-N702-15May14_S2_Aligned.sorted.bam -b CA12k_Nov2014_V4_hg19.bed > coverage.hist.BA8-n.V4.txt & | |||
/home/mzcai/softwares/bedtools-2.20.1/bin/coverageBed -counts -abam /media/LTS_33T/RL_LTS33T/201404_201405_7Samples_BulkNucleiBatch1-20140623_Expt146/STAR/RL-BA8-sec9-t-N701-15May14_S1_mapped/RL-BA8-sec9-t-N701-15May14_S1_Aligned.sorted.bam -b CA12k_Nov2014_V4_hg19.bed > coverage.counts.BA8-t.V4.txt & | |||
/home/mzcai/softwares/bedtools-2.20.1/bin/coverageBed -counts -abam /media/LTS_33T/RL_LTS33T/201404_201405_7Samples_BulkNucleiBatch1-20140623_Expt146/STAR/RL-BA8-sec9-n-N702-15May14_S2_mapped/RL-BA8-sec9-n-N702-15May14_S2_Aligned.sorted.bam -b CA12k_Nov2014_V4_hg19.bed > coverage.counts.BA8-n.V4.txt & | |||
--> | |||
/home/mzcai/softwares/bedtools-2.20.1/bin/coverageBed -abam /media/LTS_33T/RL_LTS33T/201404_201405_7Samples_BulkNucleiBatch1-20140623_Expt146/STAR/RL-BA8-sec9-t-N701-15May14_S1_mapped/RL-BA8-sec9-t-N701-15May14_S1_Aligned.sorted.bam -b CA12k_Nov2014_V4_hg19.bed > coverage.BA8-t.V4.txt & | |||
/home/mzcai/softwares/bedtools-2.20.1/bin/coverageBed -abam /media/LTS_33T/RL_LTS33T/201404_201405_7Samples_BulkNucleiBatch1-20140623_Expt146/STAR/RL-BA8-sec9-n-N702-15May14_S2_mapped/RL-BA8-sec9-n-N702-15May14_S2_Aligned.sorted.bam -b CA12k_Nov2014_V4_hg19.bed > coverage.BA8-n.V4.txt & | |||
/home/mzcai/softwares/bedtools-2.20.1/bin/coverageBed -counts -abam /media/LTS_33T/RL_LTS33T/201404_201405_7Samples_BulkNucleiBatch1-20140623_Expt146/STAR/RL-BA8-sec9-t-N701-15May14_S1_mapped/RL-BA8-sec9-t-N701-15May14_S1_Aligned.sorted.bam -b CA12k_Nov2014_V7_hg19.bed > coverage.BA8-t.V7.txt & | |||
/home/mzcai/softwares/bedtools-2.20.1/bin/coverageBed -counts -abam /media/LTS_33T/RL_LTS33T/201404_201405_7Samples_BulkNucleiBatch1-20140623_Expt146/STAR/RL-BA8-sec9-n-N702-15May14_S2_mapped/RL-BA8-sec9-n-N702-15May14_S2_Aligned.sorted.bam -b CA12k_Nov2014_V7_hg19.bed > coverage.BA8-n.V7.txt & | |||
* | *Sum up counts for each gene: CollapseSum_BedtoolsCoverageCounts.pl | ||
**e.g. coverage.BA8-n.V7.txt > coverage.BA8-n.V7.collapsed.txt | |||
=== |
Revision as of 02:43, 1 May 2015
Checking RNA-Seq Read Coverage of Probe Targets
- Probes were already filtered for those with low coverage in bulk tissue RNA-Seq with all Brodmann Areas summed together
- Still, we can check just BA8 to see if that explains lack of detection of certain genes
Create BED File for Probe Targets
- CA12kNov2014_Probelist2BED.pl
- Made start and end positions +/- 25bp from target position
- OutputFile_0gap_contig_final.full_info.V4.txt > CA12k_Nov2014_V4.bed
- OutputFile_0gap_final.full_info.V7.txt > CA12k_Nov2014_V7.bed
- Convert from hg38 reference positions to hg19 reference (which RNA-Seq data was mapped to) using UCSC LiftOver
- CA12k_Nov2014_V4.bed > CA12k_Nov2014_V4_hg19.bed
- CA12k_Nov2014_V7.bed > CA12k_Nov2014_V7_hg19.bed
Bedtools Coverage with RNA-Seq Data
- Workspace
- genome-miner:/home/mzcai/CA12kNov2014_V4_CaptureAnalysis
- genome-miner:/home/mzcai/CA12kNov2014_V7_CaptureAnalysis
- RNA-Seq data from: /media/LTS_33T/RL_LTS33T/201404_201405_7Samples_BulkNucleiBatch1-20140623_Expt146/STAR$
- RL-BA8-sec9-t-N701-15May14_S1_mapped/RL-BA8-sec9-t-N701-15May14_S1_Aligned.sorted.bam
- 59,038,666 reads
- RL-BA8-sec9-n-N702-15May14_S2_mapped/RL-BA8-sec9-n-N702-15May14_S2_Aligned.sorted.bam
- 45,222,268 reads
- RL-BA8-sec9-t-N701-15May14_S1_mapped/RL-BA8-sec9-t-N701-15May14_S1_Aligned.sorted.bam
- Commands
/home/mzcai/softwares/bedtools-2.20.1/bin/coverageBed -abam /media/LTS_33T/RL_LTS33T/201404_201405_7Samples_BulkNucleiBatch1-20140623_Expt146/STAR/RL-BA8-sec9-t-N701-15May14_S1_mapped/RL-BA8-sec9-t-N701-15May14_S1_Aligned.sorted.bam -b CA12k_Nov2014_V4_hg19.bed > coverage.BA8-t.V4.txt & /home/mzcai/softwares/bedtools-2.20.1/bin/coverageBed -abam /media/LTS_33T/RL_LTS33T/201404_201405_7Samples_BulkNucleiBatch1-20140623_Expt146/STAR/RL-BA8-sec9-n-N702-15May14_S2_mapped/RL-BA8-sec9-n-N702-15May14_S2_Aligned.sorted.bam -b CA12k_Nov2014_V4_hg19.bed > coverage.BA8-n.V4.txt & /home/mzcai/softwares/bedtools-2.20.1/bin/coverageBed -counts -abam /media/LTS_33T/RL_LTS33T/201404_201405_7Samples_BulkNucleiBatch1-20140623_Expt146/STAR/RL-BA8-sec9-t-N701-15May14_S1_mapped/RL-BA8-sec9-t-N701-15May14_S1_Aligned.sorted.bam -b CA12k_Nov2014_V7_hg19.bed > coverage.BA8-t.V7.txt & /home/mzcai/softwares/bedtools-2.20.1/bin/coverageBed -counts -abam /media/LTS_33T/RL_LTS33T/201404_201405_7Samples_BulkNucleiBatch1-20140623_Expt146/STAR/RL-BA8-sec9-n-N702-15May14_S2_mapped/RL-BA8-sec9-n-N702-15May14_S2_Aligned.sorted.bam -b CA12k_Nov2014_V7_hg19.bed > coverage.BA8-n.V7.txt &
- Sum up counts for each gene: CollapseSum_BedtoolsCoverageCounts.pl
- e.g. coverage.BA8-n.V7.txt > coverage.BA8-n.V7.collapsed.txt