Kun:LabNotes/SingleCellExpr/2015-4-25
Jump to navigation
Jump to search
Extract mapped reads from Bam files for IGV inspection
- I wrote a script for quick extraction of mapped sequencing reads near a list of genes from multiple data sets. This makes it easy to visually inspect the mapped reads with IGV, checking whether the genes/exons of interest have read coverage or not.
./extract_bam_for_selected_genes.pl gene_list data_set_folder output_folder THREE ARGUMENTS: gene_list: a plain text file containing the HUGO IDs for a list of genes, one gene per line data_set_folder: the folder that contains multiple mapped data set, each data set folder has a suffix "_mapped" output_folder: the folder where all extracted bam files will be placed.
Example: in /home/kunzhang/temp/brain_bulk_bams, run /home/kunzhang/RNAseq/SCAP/scripts/extract_bam_for_selected_genes.pl brain_selected_genes.txt \ /media/LTS_33T/RL_LTS33T/201404_201405_7Samples_BulkNucleiBatch1-20140623_Expt146/STAR .
- All the extracted bam files can be loaded into IGV for visual inspection.