[galaxy-user] Deletions

[Jennifer Jackson]

For you and other following this thread, there is one extra tool that 
can be recommended for quickly evaluating datasets: "NGS: QC and 
manipulation -> FastQC". In many cases, this can replace the other 
quality score evaluation tools.

Take care,

Jen

On 10/4/11 5:01 PM, Jennifer Jackson wrote:
> Hello Laura,
>
> On 10/3/11 11:05 AM, Laura Reinholdt wrote:
>> I have a DNA seq data set from mouse genome that is heterozygous for a
>> known 15 bp deletion. The deletion is listed in the SAM tools pileup:
>> mapping quality = 690, SNP quality =690, mapping quality =52, coverage =
>> 62, 11 reads span the deletion, 52 reads are reference. When I use SAM
>> tools ‘filter pileup on coverage and SNPs’, this deletion is filtered
>> out. I’m using the default settings for the filter: coverage=3, quality
>> cap=60 (is this the Phred quality score or is it the Phred quality
>
> The tool's form does not have an upper quality threshold, but rather a
> minimum quality score value ("Do not consider read bases with quality
> lower than:" this is defaulted to 20). The value is a Phred 33 score.
>
>> coefficient?). Does anyone whether this deletion is filtered out simply
>> because it’s a deletion or is it filtered out due to the mapping
>> quality? Can anyone suggest an alternative tool / setting for filtering
>
> If you had the minimum quality threshold set to 60, then yes, this could
> certainly have removed sequences from the region. Set this value to the
> default or to another value determined by evaluating the range of base
> qualities in your data. Use tools "NGS: QC and manipulation" -> 'Compute
> quality statistics' and 'Build base quality distribution'.
>
> Hopefully this helps,
>
> Best,
>
> Jen
> Galaxy team
>
>> the pileup?
>>
>> Thanks,
>> Laura
>>
>>
>> Laura Reinholdt, PhD
>> Research Scientist
>> Genetic Resource Sciences
>> The Jackson Laboratory
>> 600 Main Street
>> Bar Harbor, ME 04609-1500
>> (207) 288-6000, ext. 6693
>>
>>
>>
>>
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-- 
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support