[BioC] question on easyRNASeq developer version

[Nicolas Delhomme]

Hi René,

I suppose that's the email you mentioned would be on hold, right?

Nico

---------------------------------------------------------------
Nicolas Delhomme

Genome Biology Computational Support

European Molecular Biology Laboratory

Tel: +49 6221 387 8310
Email: nicolas.delhomme at embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
---------------------------------------------------------------





On Sep 27, 2012, at 10:51 AM, RenéBöttcher wrote:

>> 
>> Dear René,
>> 
>> The best place to post this - where you would get for sure my attention - is 
> the bioconductor mailing list. The
>> advantage is that other developers/users might be able to help you as your 
> message would have a better
>> visibility to the R/Bioc community. I've actually put that mailing list in Cc.
>> 
>> There indeed seem to be a sub-setting error somewhere within the function that 
> parses the read
>> information, or so I guess from your error message. Would it be possible for 
> you to share your
>> EMC_18_alignment.bam file? I can set up a folder in my dropbox for you to 
> upload the file. If that is not
>> possible, can you at least trim your bam file to the smallest size sufficient 
> to reproduce the error and
>> share that excerpt with me?
>> 
>> Best,
>> 
>> Nico
>> 
>> ---------------------------------------------------------------
>> Nicolas Delhomme
>> 
>> Genome Biology Computational Support
>> 
>> European Molecular Biology Laboratory
>> 
>> Tel: +49 6221 387 8310
>> Email: nicolas.delhomme at ...
>> Meyerhofstrasse 1 - Postfach 10.2209
>> 69102 Heidelberg, Germany
>> ---------------------------------------------------------------
>> 
>> On Sep 20, 2012, at 2:04 PM, René Böttcher wrote:
>> 
>>> Dear Mr. Delhomme,
>>> 
>>> I would like to ask for your support concerning a problem I'm facing when 
> using your easyRNASeq package.
>> There seems to be an issue in one of the subfunctions, 
>>> however, I am not able to tell which one, as the error message is rather 
> short.
>>> 
>>> "Error in mk_singleBracketReplacementValue(x, value) : 
>>> 'value' must be a CompressedIntegerList object"
>>> 
>>> Please not that I'm trying to follow the example cases you provided and I am 
> currently using the developer
>> version since my alignments require multiple reads length support according to 
> your current stable
>> release. You can find a detailed problem description on Seqanswers, as it 
> seems I am not the only one
>> encountering this problem.
>>> 
>>> http://seqanswers.com/forums/showthread.php?t=23477
>>> 
>>> With kind regards,
>>> René Böttcher
>> 
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>> 
>> 
> 
> 
> Dear Nicolas,
> 
> I ran picard-tools FixMateInformation on my bam-file, however, it did not solve 
> the problem. Additionally, the problem also occurs with another sample, so I 
> will now crop both of these bam-files to reduce their size and still retain 
> reproducibility. If you could provide me with your dropbox folder, I can then 
> upload them for you to test where the bug occurs.
> 
> Thank you for your support.
> 
> With kind regards,
> René
> 
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