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  • carmeyeii
    replied
    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

    Leave a comment:


  • Zaag
    replied
    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.

    Leave a comment:


  • matan8
    replied
    How do you use the command line to map the data? I am looking for examples for that, but can't find any.

    Leave a comment:


  • AmitL
    replied
    If you say so, I might give it a second chance.

    Thank you

    Leave a comment:


  • golharam
    replied
    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.

    Leave a comment:


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

    Leave a comment:


  • golharam
    replied
    Just out of curiosity, why are you not using LifeScope?

    Leave a comment:


  • yksikaksi
    replied
    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.

    Leave a comment:


  • AmitL
    replied
    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!

    Leave a comment:


  • yksikaksi
    replied
    Have you consider to map your csfasta reads with SHRiMP2?

    Leave a comment:


  • AmitL
    replied
    Alright. Thanks a lot!

    Leave a comment:


  • nilshomer
    replied
    Originally posted by AmitL View Post
    How do you know it's meant for mate-pairs?

    On the documentation it says:
    Check out the source code "bwape.c" and search for SOLID. It uses the F3/R3 "pairing", which is mate pair.

    Leave a comment:


  • AmitL
    replied
    How do you know it's meant for mate-pairs?

    On the documentation it says:
    Generate alignments in the SAM format given paired-end reads.

    Leave a comment:


  • nilshomer
    replied
    The new version does not work with color space. The older version works with mate pairs and color space, but not paired end and color space.

    Leave a comment:


  • AmitL
    replied
    I know the new version does not work with color-space.
    Are you saying that it's true for the older versions too?

    Leave a comment:

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