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Abhimanyu Singh's questions

  • Abhimanyu Singh
    34 days ago
    Questions (1)

    MIRA produces contigs with varied names:

    1)>projName_c[number] 2)>projName_rep_c[number]

    What is the difference between these two types of consensus sequences?

  • Abhimanyu Singh
    140 days ago
    Questions (3)

    I mapped reads with
    bwa mem -M -t 40 allCombinedFinalSet.fa Seq.R1.fastq Seq.R2.fastq > aln.sam
    

    Extracted the mapped reads

    samtools view -f 0x2 -b aln.bam > output.bam
    

    Extracted the fastq

    bamToFastq -i output.bam -fq R1.fq -fq2 R2.fq 
    
    grep @HISEQ578:1035:HJ2KCBCXX:1:1104:14672:39678/1 R1.fq             []
    @HISEQ578:1035:HJ2KCBCXX:1:1104:14672:39678/1
    @HISEQ578:1035:HJ2KCBCXX:1:1104:14672:39678/1
    @HISEQ578:1035:HJ2KCBCXX:1:1104:14672:39678/1
    

    I notice it has duplicated ....

    I think this because read was mapped twice (i.e. BWAmem).

    I tried fastuniq but it does not remove the duplicated reads.

    Can you please help me to remove duplicated reads from fastq files.

  • Abhimanyu Singh
    231 days ago
    Questions (2)

    I got the following error while running MizBee.How to fiw it.

    ./MizBee                                    []
    OpenJDK 64-Bit Server VM warning: You have loaded library /home/abhi/Downloads/application.linux(1)/application.linux/libgluegen-rt.so which might have disabled stack guard. The VM will try to fix the stack guard now.
    It's highly recommended that you fix the library with 'execstack -c ', or link it with '-z noexecstack'.
    Exception in thread "Animation Thread" java.lang.UnsatisfiedLinkError: /home/abhi/Downloads/application.linux(1)/application.linux/libgluegen-rt.so: /home/abhi/Downloads/application.linux(1)/application.linux/libgluegen-rt.so: wrong ELF class: ELFCLASS32 (Possible cause: architecture word width mismatch)
        at java.lang.ClassLoader$NativeLibrary.load(Native Method)
        at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1941)
        at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1857)
        at java.lang.Runtime.loadLibrary0(Runtime.java:870)
        at java.lang.System.loadLibrary(System.java:1122)
        at com.sun.gluegen.runtime.NativeLibLoader.loadLibraryInternal(NativeLibLoader.java:102)
        at com.sun.gluegen.runtime.NativeLibLoader.access$000(NativeLibLoader.java:51)
        at com.sun.gluegen.runtime.NativeLibLoader$1.run(NativeLibLoader.java:70)
        at java.security.AccessController.doPrivileged(Native Method)
        at com.sun.gluegen.runtime.NativeLibLoader.loadGlueGenRT(NativeLibLoader.java:68)
        at com.sun.gluegen.runtime.NativeLibrary.ensureNativeLibLoaded(NativeLibrary.java:399)
        at com.sun.gluegen.runtime.NativeLibrary.open(NativeLibrary.java:163)
        at com.sun.gluegen.runtime.NativeLibrary.open(NativeLibrary.java:129)
        at com.sun.opengl.impl.x11.DRIHack.begin(DRIHack.java:109)
        at com.sun.opengl.impl.x11.X11GLDrawableFactory.(X11GLDrawableFactory.java:99)
        at java.lang.Class.forName0(Native Method)
        at java.lang.Class.forName(Class.java:264)
        at javax.media.opengl.GLDrawableFactory.getFactory(GLDrawableFactory.java:111)
        at processing.opengl.PGraphicsOpenGL.allocate(PGraphicsOpenGL.java:173)
        at processing.core.PGraphics3D.setSize(PGraphics3D.java:323)
        at processing.core.PApplet.makeGraphics(PApplet.java:1321)
        at processing.core.PApplet.size(PApplet.java:1142)
        at processing.core.PApplet.size(PApplet.java:1102)
        at MizBee.setup(MizBee.java:87)
        at processing.core.PApplet.handleDraw(PApplet.java:1571)
        at processing.core.PApplet.run(PApplet.java:1496)
        at java.lang.Thread.run(Thread.java:745)

  • Abhimanyu Singh
    381 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.