how can i determine the couverture (coverage ) of my reads on the whole genome using mapping (bowtie2)

Question

[Bioinfo]

Hello Biostar PLease i have question i build database using different genome references of differents bacteria strains i want to determine the coverage of my reads on the this database can i do that by mapping the reads against the database

Thank you very much

[GenoMax]

i build database using different genome references of differents bacteria strains

Are these databases separate? Do your samples contain only one bacteria at a time?

If the answer is no to either or both then you are going to wrestle with the issue of multi-mapping reads. Many bacterial genomes are going to share sequences and that will make data alignments complex and will affect the "coverage" in a big way.

[Bioinfo]

Hello thank you for your reply , yes , these databases are separated , because i downloaded all the fasta file i found about genre of the bacteria from ncbi then i merge all the files in one file , and i build the database using it and yes i guess you're right because i found that 63% of my reads are aligned more than one time

i don't know if it s okay to use just one fasta file to build the database how can i avoid this problem please ? Thank you

[GenoMax]

yes , these databases are separated , because i downloaded all the fasta file i found about genre of the bacteria from ncbi then i merge all the files in one file , and i build the database using it

That statement is conflicting. Do you have separate bowtie2 indexes for each genome or a common index for all genomes?

Answer 1

[Istvan Albert]

Map the reads to the genomes then use

bedtools genomecov

to figure out the coverage from the resulting alignment files. Simpler coverages can be summarized with

samtools flagstat

or

samtools idxstats

[Bioinfo]

Thank you very much for your answer