Matt:LabNotes/2015-4-27: Difference between revisions
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>Mzcai (Created page with "==Checking RNA-Seq Read Coverage of Probe Targets== *[[Matt:LabNotes/2014-11-1#Filter_Probes_with_Low_Coverage_based_on_Brain_RNA-seq_Data_from_Rui.2FBlue | Probes were alread...") |
>Mzcai |
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*[[Media:CA12kNov2014_Probelist2BED.txt |CA12kNov2014_Probelist2BED.pl]] | *[[Media:CA12kNov2014_Probelist2BED.txt |CA12kNov2014_Probelist2BED.pl]] | ||
**Made start and end positions +/- 25bp from target position | **Made start and end positions +/- 25bp from target position | ||
**[[Media:OutputFile_0gap_contig_final.full_info.V4.txt|OutputFile_0gap_contig_final.full_info.V4.txt]] > [[Media | **[[Media:OutputFile_0gap_contig_final.full_info.V4.txt|OutputFile_0gap_contig_final.full_info.V4.txt]] > [[Media:CA12k_Nov2014_V4.txt|CA12k_Nov2014_V4.bed]] | ||
**[[Media:OutputFile_0gap_final.full_info.V7.txt|OutputFile_0gap_final.full_info.V7.txt]] > CA12k_Nov2014_V7.bed | **[[Media:OutputFile_0gap_final.full_info.V7.txt|OutputFile_0gap_final.full_info.V7.txt]] > CA12k_Nov2014_V7.bed | ||
Revision as of 03:06, 28 April 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
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
- RL-BA8-sec9-n-N702-15May14_S2_mapped/RL-BA8-sec9-n-N702-15May14_S2_Aligned.sorted.bam
- Commands
/home/mzcai/softwares/bedtools-2.20.1/bin/coverageBed -hist -abam RL-BA8-sec9-t-N701-15May14_S1_mapped/RL-BA8-sec9-t-N701-15May14_S1_Aligned.sorted.bam -b CA12k_Nov2014_V4.bed >