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  • How to get name and sequence of reads mapped to a particular gene
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 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 ?






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  1. The intersection between a gtf file of the reference annotation and the reads without further ado will probably retrieve all reads (mates) that overlap exons. The annotation mapping of flux is slightly different, it employs reads that fall within exons and form valid pairs. As there is currently no user option to output reads and their sequences, I filed a Request for Improvement

    Unable to locate Jira server for this macro. It may be due to Application Link configuration.

    I hope we can soon provide a solution.




    1. Jin

      Thank you very much for your reply!

      I will keep my eyes open for any updates (smile)