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  • #16
    Originally posted by AmitL View Post
    Yes.
    Shrimp2 collapses because of non-existing input problems. I have checked the input manually and it was ok. It works with all other tools.

    I preferred not to deal with such a buggy tool.

    But thanks!
    Hum... it is strange. I managed to map my csfasta reads with SHRiMP2 but not BWA.

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    • #17
      Just out of curiosity, why are you not using LifeScope?

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      • #18
        Did you try it?
        Its interface is very uncomfortable and it cannot be fully operated through shell scripts.

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        • #19
          I agree. I only use LifeScope to map data, and I use the command-line interface. The GUI is horrible. Once I have the BAM files I do the rest of my processing outside of LifeScope.

          I ask because I keep hearing LifeScope does a better job mapping reads than other tools. I haven't tried others myself though.

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          • #20
            If you say so, I might give it a second chance.

            Thank you

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            • #21
              How do you use the command line to map the data? I am looking for examples for that, but can't find any.

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              • #22
                From the manual (buildup of the manual is as horrible as the GUI):

                1. Create a text file with one command per line. For example:
                cd proj1
                cd run2
                set workflow analysis.pln
                add xsq xsqfile
                set reference hg19
                run
                ls
                exit

                2. Save the file, for example as proj1script.

                3. Then run with this command:
                lscope.sh -u user -w password < proj1script

                Note: This example does not include the commands necessary to step up a new analysis.


                See page 78 of the Command shell user guide, there are several other/easier ways if you have standard pipelines.

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                • #23
                  Hi!

                  I'm analyzing a "second-hand" dataset generated using SOLiD 4. It is a transcriptome mate pair library that is 52 x 37 nt, and I cannot for the sake of me find the protocol that was used to generate those specific read lengths. I have F3 and R3 reads, so I am assuming it is a circularization protocol, but I do not know what the size selection parameters were, or how the circles were cut to produce the final fragments. This info would be very valuable for a more accurate mapping.

                  Any knowledge would be greatly appreciated!

                  Thanks a lot,

                  Carmen

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