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

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

rna-seq transcription
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updated by khorms khorms • written by Chvatil Chvatil

1 answer

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

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written by khorms khorms

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

• 0 views • link
written by Chvatil Chvatil

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