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  • searching tools and informations about 4C seq analysis

    Hi,
    Do we have any news about 4C seq analysis tools?
    I am trying to use one tool with the name 4cseqpipe available here http://compgenomics.weizmann.ac.il/tanay/?page_id=367.
    Does anyone used this for a data set?

  • #2
    Hi,

    I am also using 4cseqpipe but getting the message
    Mapper will quit now. Please reduce the value for "min_precision_for_weight" setting and run again the program.
    Also beware that you might experience slow run-times with low quality reads.
    To improve run-times consider lowering down the precision by reducing the value of "max_mismatches".

    But there is no option to change the values of these parameters.
    Anyone has any idea?

    thanks
    shruti

    Comment


    • #3
      Hey Shruti,

      I'm having the same issue going into mapping "Mapper will quit now..."

      I'll let you know if I come up with anything, but does anyone else have any input? I don't see this issue with the example data but I'm not sure if it's data quality or a pipeline issue yet. I'm trying to just trim and map with bowtie myself just as a sanity check. The read structure and fastqc look okay at least...

      Comment


      • #4
        So for me the issue was with the quality score encoding. Try using "-convert_qual" when running the first stage of the pipeline. Weird that the error message was about mapping precision, but I'm glad it's fixed at least.

        As far as I can tell "min_precision_for_weight" is hardcoded in the C++ mapper.

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        • #5
          Thanks ranting_swede,

          will try and let you know. I guess I misunderstood the function of the parameter "-convert_qual" before.

          Comment


          • #6
            Hi...
            just to report.. my problem was solved by using the parameter -convert_qual 1

            Comment


            • #7
              Hi,

              For some of my samples while running 4cseqpipe I am running into the following error:

              Error in approx(bd$start, uni_cut_3, n = length(bd$start)) :
              need at least two non-NA values to interpolate
              Execution halted

              Anyone has an idea what to do? or check?
              Thanks

              shruti

              Comment

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