High coverage, suspecting a problem...

[lindenb]

We've sequenced an exome (SureSelect) with our HiSeq .

I've aligned the reads with bwa & marked the duplicates. the qualities of the reads seem to be OK.

I'm puzzled: I've got a very high coverage in the target regions (mean: ~150/200) and I'm looking for a way to explain it.

For a sample the size of the FASTQs is 10Gb.
Whereas for a previous sequencing of the same sample the size of the FASTQs was 4.G (The size of the illumina folder was ~150Gb with both folders).

What would you suggest to explore the reason of this high coverage ?

I've extracted my FASTQs using the following command (with the default options):

${CASAVADIR}/bin/configureBclToFastq.pl \
	--input-dir ${BCLDIR}/Data/Intensities/BaseCalls \
	--output-dir ${FASTQDIR} \
	--sample-sheet ${BCLDIR}/SureSelect2.csv \
	--force

should have I used some other options ?


Thanks,

Pierre

[share]

I am not expert in bioinformatics before going further I suggest you to compare the cluster numbers and millions of reads of both flow cells. If they both are same then I guess you may have to look at the bioinformatics steps.