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):
should have I used some other options ?
Thanks,
Pierre
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):
Code:
${CASAVADIR}/bin/configureBclToFastq.pl \ --input-dir ${BCLDIR}/Data/Intensities/BaseCalls \ --output-dir ${FASTQDIR} \ --sample-sheet ${BCLDIR}/SureSelect2.csv \ --force
Thanks,
Pierre
Comment