I am trying to look at some of the actual reads that mapped to a particular gene using the GEUVADIS data set.
For example, lets say I have a bed file for one individual (SAMPLE1.bed) and the gencode annotation file (GENCODE.v12.gtf). I would like the output to be bed file oriented like this:
Mappedread_ID Mappedread_Chr Mappedread_start Mappedread_end Mappedread_sequence Gene_ID Gene_chromosome Gene_start Gene_end
HWI-ST:XXXXX 1 15000 15020 ATTTATATGATTTATATAT ENSG000001234 Chr 1 14000 16000
With my limited understanding about flux-capacitor, it seems to me that its main purpose is to generate read counts for each gene and does not return the actual read ID's which mapped to a certain gene.
I managed to do this in bedtools by using the following command, but wasn't sure if bedtools and flux-capacitor are operating in the same fashion.
bedtools intersect -a SAMPLE1.bed -b GENCODE.v12.gtf -wb > output.txt
Is the equivalent to the above possible using flux capacitor ?