[BioC] question on easyRNASeq developer version

RenéBöttcher r.bottcher at erasmusmc.nl
Thu Sep 27 10:51:07 CEST 2012

> 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 
> > 
> > "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,

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