Test if a list of genes with coordinates are expressed (hisat2 data)

Question

[Chvatil]

Hello everyone, I need some help in order to know wether candidates genes are expressed or not.

In order to do that I have already done the following steps :

3 Built hisat indexes

  $HISAT2/hisat2-build Assembly.fa mapping_index

2 Mapper the RNA reads to the assembly

$HISAT2/hisat2 --dta -k 1 -q -x mapping_index --sra-acc SRR6456290,SRR6456292  | $SAMTOOLS/samtools view -o mapping_Assembly.bam 2> stats_mapping.txt

3) Sorted bam by position

$SAMTOOLS/samtools sort mapping_Assembly.bam -o mapping.sorted_Assembly.bam

and I have a list of candidate genes with coordinates such as :

Exemple

Chr start end strand 
1 1 600 -
1 200 90 -
2 30 900 +

and I would like to know if these particular genes are significatively expressed or not ? I know that a TMP method could be a nice idea but I do not know what kind of program is the most suitable for my question ? I do not want to test for difference of expression within conditions, just to test if the candidat gene is exprimed.

Thank you very much for you help

[ATpoint]

There is no gold standard to determine when a gene is expressed or not. There is often background transcriptional level, especially detected when samples are sequenced deeply, but without biological meaning. For a data-driven method check for example zFPKM: https://www.bioconductor.org/packages/release/bioc/html/zFPKM.html

Answer 1

[khorms]

You could use IGV to visualize both your alignment .bam file and your bed file; this way you could manually inspect the regions of interest

[Chvatil]

Thanks but I have around thousand of candidate gene and I need to get a more general method ..