BOL

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

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.

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

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

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.

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

I would like to extract a subset of PE reads (50%) and store them in seperate files. It should be in both way "split by middle" or "random". Is there any way to achieve it?

Hi There, 

I recently came across a new term "phasing". What does it mean? I only know it means "genes separated by chromosome" only, can anyone please explain it for me.

Thanks in advance.

MIRA follows for the ref based assembly (like mapping the reads on the reference with xxx, etc.) and if its possible to have a figure with the workflow.