[Bioc-sig-seq] Assessing Transcriptome Coverage

[Abhishek Pratap]

Hi Michael

Thanks for your reply. Well basically we have downloaded the human
reference RNA set from NCBI and using the same to asses coverage. It
is a rough estimate to help our collaborators decide on hwo much
sequencing they need to do in order to reach required coverage for SNP
calling. So till now I have calculated coverage using the ELAND
alignment results. I am now looking for ways to plot it so that
biologists could interpret it easily.

So I have many hashes(perl), each having a "numerical" coverage data
obtained from Next generation sequencing data analysis. Now each
hash/list may have couple of hundred to thousands entry "contig_name
=> coverage".  What I want to do is to plot a histogram for each
hash/dataset.  "Coverage v/s Count of contigs with coverage > #N " ( N
has to be binned according to the data size).

Any pointers in this regard will help a lot.

Thanks,
-Abhi




On Thu, Aug 13, 2009 at 4:30 AM, Michael
Dondrup<Michael.Dondrup at bccs.uib.no> wrote:
> Hi Abhi,
>
> just a short comment. To assess coverage the crucial point is to know the
> length of your target sequence, thus the length of the
> human transcriptome. Then e.g. the Lander-Waterman statistic can be
> computed. So how could the length of total mRNA
> be calculated. I think this is not possible, is it?
>
> Best
> Michael
>
> Am 12.08.2009 um 23:59 schrieb Abhishek Pratap:
>
>> Hi All
>>
>> Just wondering if a package/R function exists which can help us answer
>> the following question.
>>
>> We are trying to assess the right amount of sequencing we need to do
>> in order to cover the human transcriptome.  For the runs we have
>> already done, we have the reads aligned to human mrna ref using ELAND.
>> We would like to plot graphs per lane to show the percent coverage of
>> human transcriptome.
>>
>> Let me know if it is not clear, I can reframe or explain in detail.
>>
>> Thanks,
>> -Abhi
>>
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>
>