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Bulbul's questions

  • Bulbul
    203 days ago
    Questions (3)

    I wanted to remove the duplicates from fastq file. I planned to use fastuniq but it does not have good tutorial. Can you please tell me how to use it?

    http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0052249

  • Bulbul
    210 days ago
    Questions (1)

    Looking for files named in data ...Pushing back filename: "clean_a2017.R1.fq"
    Could not determine filetype from data 'clean_Avaga2017.R1.fq' ("clean_a2017.R1.fq")
    Pushing back filename: "clean_a2017.R2.fq"
    Could not determine filetype from data 'clean_a2017.R2.fq' ("clean_a2017.R2.fq")

    Fatal error (may be due to problems of the input data or parameters):

    ********************************************************************************
    * Some 'data' entries named in the manifest file could not be verified, see *
    * the log above. *
    * Maybe some files are missing, not readable or there is a typo in the *
    * manifest file? *
    ********************************************************************************

  • Bulbul
    333 days ago
    Questions (1)

    make[3]: Entering directory '/home/dept/Tools/amos-3.1.0/src/Align'
    g++ -DHAVE_CONFIG_H -I. -I../..  -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation   -g -O2 -MT find-tandem.o -MD -MP -MF .deps/find-tandem.Tpo -c -o find-tandem.o find-tandem.cc
    find-tandem.cc: In function ‘int main(int, char**)’:
    find-tandem.cc:243:3: error: ‘optarg’ was not declared in this scope
       optarg = NULL;
       ^
    find-tandem.cc:245:63: error: ‘getopt’ was not declared in this scope
       while (!errflg && ((ch = getopt (argc, argv, "f:u:l:x:m:k:h")) != EOF))
                                                                   ^
    find-tandem.cc:258:55: error: ‘optopt’ was not declared in this scope
             fprintf (stderr, "Unrecognized option -%c\n", optopt);
                                                           ^
    Makefile:918: recipe for target 'find-tandem.o' failed
    make[3]: *** [find-tandem.o] Error 1
    make[3]: Leaving directory '/home/urbe/Tools/amos-3.1.0/src/Align'
    Makefile:325: recipe for target 'all-recursive' failed
    make[2]: *** [all-recursive] Error 1
    make[2]: Leaving directory '/home/urbe/Tools/amos-3.1.0/src'
    Makefile:306: recipe for target 'all-recursive' failed
    make[1]: *** [all-recursive] Error 1
    make[1]: Leaving directory '/home/urbe/Tools/amos-3.1.0'
    Makefile:244: recipe for target 'all' failed
    make: *** [all] Error 2

  • Bulbul
    345 days ago
    Questions (1)

    Using breakdancer the output consists of DEL, INV, INS, CTX and ITX. Using following commands:

    bam2cfg.pl -g -h dis.bam normal.bam > config_file.cfg
    breakdancer_max -d test config_file.cfg > dis_normal.ctx

    the 11th output column should displays the amount of reads supporting the called SV per bam-file. I have some unusual research in 11th column, can you please helpme to fix it.