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All site questions

  • Poonam Mahapatra
    171 days ago
    Questions (1)

    I tried SyMAP but got the following error 

    $ ./symap []

    Starting SyMAP v4.2 - Project Manager
    SyMAP Version v4.2
    Java Version 1.8.0_91, mem: 1820M
    Build 116
    Reading from file symap.config
    The built-in MySQL server cannot run because a MySQL server is already running on this computer.
    Please stop that server, or else specify a MySQL host name in the symap.config file.

  • pradyumna Jayaram
    200 days ago
    Questions (1)

    If i have a set of miRNA sequences, what are the tools that are available to predict the target genes? I tried miRanda and mirdb, are there any  tools or databases that do the same, as the rna is not already known i cant use targetscan etc. The tool must predict the target from the fasta sequence of miRNA.

    Thank you

  • Neelam Jha
    211 days ago
    Questions (4)

    I am trying to merge contigs, generated from different assemblies with MeGAMerge, but it failed after running few hour !! Following are the error I got on command prompt. Any suggestions??

    perl MeGAMerge-1.1.pl -f MergedDIR allContigs_MIRA_assembled.fa
    Running Newbler assembly with 308261 sequences
    runAssembly -force -large -rip -mi 98 -ml 80 -pairt -cpu 4 -a 200 -o MergedDIR/newbler MergedDIR/newblerIn.fasta 1>/dev/null 2>/dev/null
    Running Minimus2 with 331388 sequences
    minimus2 -D CONSERR=0.06 -D MINID=98 -D OVERLAP=80 MergedDIR/minimus.fasta 1>/dev/null 2>/dev/null
    minimus2 -D CONSERR=0.06 -D MINID=98 -D OVERLAP=80 MergedDIR/minimus.fasta 1>/dev/null 2>/dev/null failed:
    Died at MeGAMerge-1.1.pl line 283.

  • Bulbul
    211 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
    223 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.


  • Tayyba Jadoon
    315 days ago
    Questions (2)

    Anyone PhD here ?  I need help in protein structure prediction.

  • Shruti Paniwala
    318 days ago
    Questions (4)

    I am working on assembly of new genome. I am just wondering how to validate my assembled genome? 

  • Abhimanyu Singh
    320 days ago
    Questions (2)

    Looking for list of human SNPs associated with a disease? We need to evaluate a large number of human SNPs for their possible association with a disease. So far, the closest I've seen is SNPedia, but a database would be more helpful.

  • Hardeep Kaur
    326 days ago
    Questions (1)

    How to intrepet the FASTQ files? What does Q score mean? Does + have any meanings?