Hi All,
I have recently experienced a problem using the human GRCh37/hg19 assembly (from UCSC) with CASAVA/Eland.
After aligning samples with an expected random coverage to the UCSC GRCh37/hg19 assembly, we noticed large areas with zero read coverage. For example no hits were found between positions 1 and
151000000 on chr1.
The fix to this was to place all of the random and unplaced contigs from the assembly into one file before squashing the genome. After we had reduced the number of reference files our alignment ran as expected, and produced the whole genome coverage we expected to see. I was wondering if anyone else has experienced anything similar?
I have recently experienced a problem using the human GRCh37/hg19 assembly (from UCSC) with CASAVA/Eland.
After aligning samples with an expected random coverage to the UCSC GRCh37/hg19 assembly, we noticed large areas with zero read coverage. For example no hits were found between positions 1 and
151000000 on chr1.
The fix to this was to place all of the random and unplaced contigs from the assembly into one file before squashing the genome. After we had reduced the number of reference files our alignment ran as expected, and produced the whole genome coverage we expected to see. I was wondering if anyone else has experienced anything similar?
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