[BioC] wishlist for readGappedAlignments
mtmorgan at fhcrc.org
Tue Aug 23 22:47:07 CEST 2011
Hi Tengfei --
We've acted on some of your suggestions (e.g., incorporating any field
in GappedAlignments, making readBamGappedAlignments accept a
ScanBamParam() when Rsamtools 1.5.53 becomes avaiable), thanks!
We're really interested in hearing from you and others about specific
use cases for paired-end representations, particularly those operations
that are difficult to do with the current GappedAlignments (e.g., the
distribution of insertion sizes could now be easily extracted as
So please forward any specific use cases!
On 08/09/2011 11:33 AM, Tengfei Yin wrote:
> Dear all,
> I am using GenomicRanges and Rsamtools a lot for my work, they are extremely
> helpful and neat packages to deal with NGS data, thanks a lot for those
> people how contribute to all those nice packages in BioC. I just have some
> features request for the GappedAlignments, probably it's already there or
> it's not a good practice to do it in certain way, please feel free to let me
> I like features from both scanBam or readBamGappedAlignments, just sometime
> I need to write my own script trying to combine information from those two
> function and make a "general" granges to work with. So I am wondering if
> there is any way to do it in a neat way or is there a plan to implement
> similiar features?
> - Including more element meta data with GappedAlignments
> - there is "which" in readBamGappedAlignments, can I have some thing
> like "param" or "what" to get more info from bam file and associate them
> with Gapped reads.
> - When doing the coerce from GappedAlignement to GRanges, or call
> granges() on GappedAlignments object, it only return the minimal
> information, "qwidth", "cigar", "ngap" is not included as
> - Including more pairing information for pair-end RNA-seq
> - So I could know the mated information with certain gapped reads,
> either plot it as pair-end read or do some computation on it.
> - Setting flags for each entry, so I can filter it out based on the
> flags, something like from scanBamFlag?
> - grglist to transform the data in different way
> If I can get a general data structure which combine all those information
> and or features together, that would be nice, I realize it's hard to
> combine all information together and make it flexible at the same time ,
> e.g. you need to deal with how to binding element meta data for paired
> entry, probably showing seq1/seq2 to indicate which sequence it's belongs
> too? how to handle multiple hits?
> Right now, I am making my own "giant" GRanges object which including all the
> information I want, but that's too specific for my work, that's why I am
> wondering if there is any plan to combine those neat features together and
> bring a more flexible data structure.
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