<![CDATA[BOL: All site questions]]> https://bioinformaticsonline.com/answers/?offset=100 https://bioinformaticsonline.com/answers/view/30365/why-megamerge-terminated-with-minimusfasta-1devnull-2devnull-failed-error Fri, 23 Dec 2016 14:11:00 -0600 https://bioinformaticsonline.com/answers/view/30365/why-megamerge-terminated-with-minimusfasta-1devnull-2devnull-failed-error <![CDATA[Why MeGAMerge terminated with minimus.fasta 1>/dev/null 2>/dev/null failed: error]]> 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.

]]> Neel https://bioinformaticsonline.com/answers/view/30353/how-to-resolve-following-amos-installation-error Fri, 23 Dec 2016 08:30:34 -0600 https://bioinformaticsonline.com/answers/view/30353/how-to-resolve-following-amos-installation-error <![CDATA[How to resolve following Amos installation error ?]]> 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 https://bioinformaticsonline.com/answers/view/30107/why-breakdancer-does-not-displays-the-amount-of-reads-supporting-sv Sat, 10 Dec 2016 16:44:38 -0600 https://bioinformaticsonline.com/answers/view/30107/why-breakdancer-does-not-displays-the-amount-of-reads-supporting-sv <![CDATA[Why BreakDancer does not displays the amount of reads supporting SV?]]> 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.


]]> Bulbul https://bioinformaticsonline.com/answers/view/29164/which-are-the-best-known-web-server-for-protein-structure-prediction Sat, 10 Sep 2016 11:26:42 -0500 https://bioinformaticsonline.com/answers/view/29164/which-are-the-best-known-web-server-for-protein-structure-prediction <![CDATA[Which are the best known web server for protein structure prediction?]]> Anyone PhD here ?  I need help in protein structure prediction.

]]> Tayyba Jadoon https://bioinformaticsonline.com/answers/view/29118/how-to-validate-the-assembly Wed, 07 Sep 2016 03:27:12 -0500 https://bioinformaticsonline.com/answers/view/29118/how-to-validate-the-assembly <![CDATA[How to validate the assembly?]]> I am working on assembly of new genome. I am just wondering how to validate my assembled genome? 

]]> Shruti Paniwala https://bioinformaticsonline.com/answers/view/29022/is-there-a-list-of-human-snps-associated-with-a-disease Mon, 05 Sep 2016 04:28:09 -0500 https://bioinformaticsonline.com/answers/view/29022/is-there-a-list-of-human-snps-associated-with-a-disease <![CDATA[Is there a list of human SNPs associated with a disease?]]> 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.

]]> Abhimanyu Singh https://bioinformaticsonline.com/answers/view/28931/how-to-intrepet-the-fastq-files Tue, 30 Aug 2016 05:54:01 -0500 https://bioinformaticsonline.com/answers/view/28931/how-to-intrepet-the-fastq-files <![CDATA[How to intrepet the FASTQ files?]]> How to intrepet the FASTQ files? What does Q score mean? Does + have any meanings? 

]]> Hardeep Kaur https://bioinformaticsonline.com/answers/view/28899/how-can-i-get-the-allele-frequency-of-my-variant Fri, 26 Aug 2016 03:20:06 -0500 https://bioinformaticsonline.com/answers/view/28899/how-can-i-get-the-allele-frequency-of-my-variant <![CDATA[How can I get the allele frequency of my variant?]]> Shruti Paniwala https://bioinformaticsonline.com/answers/view/28830/how-to-extract-50-of-the-reads Thu, 18 Aug 2016 03:20:27 -0500 https://bioinformaticsonline.com/answers/view/28830/how-to-extract-50-of-the-reads <![CDATA[How to extract 50% of the reads?]]> 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?

]]> Radha Agarkar https://bioinformaticsonline.com/answers/view/28393/what-does-phasing-mean-in-biologygenetics Mon, 11 Jul 2016 04:29:37 -0500 https://bioinformaticsonline.com/answers/view/28393/what-does-phasing-mean-in-biologygenetics <![CDATA[What does phasing mean in biology/genetics?]]> 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.

]]> Priya Singh