<![CDATA[BOL: All site questions]]> https://bioinformaticsonline.com/answers/?offset=60 https://bioinformaticsonline.com/answers/view/36454/what-are-the-best-method-to-validate-genome-assembly Mon, 30 Apr 2018 04:32:56 -0500 https://bioinformaticsonline.com/answers/view/36454/what-are-the-best-method-to-validate-genome-assembly <![CDATA[What are the best method to validate genome assembly ?]]> I am working on a metazoan genome. I wanted to try the best known method to validate the assembly structure. Your suggestions are welcome. 

]]> Seema Singh https://bioinformaticsonline.com/answers/view/36250/how-to-install-perl-gd-module-in-ubuntu Tue, 17 Apr 2018 08:46:53 -0500 https://bioinformaticsonline.com/answers/view/36250/how-to-install-perl-gd-module-in-ubuntu <![CDATA[How to install Perl GD module in Ubuntu ?]]> While installing Perl GD module, I got following error 

libgd not found !

 

]]> Shruti Paniwala https://bioinformaticsonline.com/answers/view/35891/unable-to-index-fasta-file-with-samtools Wed, 07 Mar 2018 16:44:10 -0600 https://bioinformaticsonline.com/answers/view/35891/unable-to-index-fasta-file-with-samtools <![CDATA[Unable to index fasta file with samtools !]]> I am unable to index fasta file with samtools ! It return "different line length in sequence" error message . How to fix it? 

nc@radha[Downloads] samtools faidx dedup.genome.scf.fasta_assembly.fna []
[fai_build_core] different line length in sequence 'jcf7180000001219'.
Could not build fai index dedup.genome.scf.fasta_assembly.fna.fai
nc@radha[Downloads] more dedup.genome.scf.fasta_assembly.fna| grep ">" | wc -l
336

]]> Radha Agarkar https://bioinformaticsonline.com/answers/view/35567/how-to-plot-a-circular-overlapping-plots-in-circos Tue, 13 Feb 2018 07:25:35 -0600 https://bioinformaticsonline.com/answers/view/35567/how-to-plot-a-circular-overlapping-plots-in-circos <![CDATA[How to Plot a circular overlapping plots in Circos ?]]> How to Plot a circular overlapping plots, as shown in pic. ?

https://cloud.githubusercontent.com/assets/90373/13977453/0ba63268-f0ef-11e5-9b1b-6b0aa587e3ac.jpg

I tried following table to plot on http://mkweb.bcgsc.ca/tableviewer/

data C D
A 7 18
B 5 15

and it return http://mkweb.bcgsc.ca/tableviewer/tmp/fvufmlm/results/circos-table-fvufmlm-large.png but it does not support overlaps. Any suggestions ?

]]> Radha Agarkar https://bioinformaticsonline.com/answers/view/35435/how-to-fix-the-macos-error-for-%E2%80%98ddalpha%E2%80%99-r-package-installation Sat, 03 Feb 2018 09:18:52 -0600 https://bioinformaticsonline.com/answers/view/35435/how-to-fix-the-macos-error-for-%E2%80%98ddalpha%E2%80%99-r-package-installation <![CDATA[How to fix the MacOS error for ‘ddalpha’ R package installation ?]]> > install.packages(c('ddalpha', 'recipes')) 

  There is a binary version available but the source version is later:

        binary  source needs_compilation

ddalpha  1.3.1 1.3.1.1              TRUE

 

Do you want to install from sources the package which needs compilation?

y/n: y

trying URL 'https://mirrors.nic.cz/R/bin/macosx/el-capitan/contrib/3.4/recipes_0.1.2.tgz'

Content type 'application/octet-stream' length 998818 bytes (975 KB)

==================================================

downloaded 975 KB

 

 

The downloaded binary packages are in

/tmp/RtmpUg5Cs2/downloaded_packages

installing the source package ‘ddalpha’

 

trying URL 'https://mirrors.nic.cz/R/src/contrib/ddalpha_1.3.1.1.tar.gz'

Content type 'application/octet-stream' length 543279 bytes (530 KB)

==================================================

downloaded 530 KB

 

* installing *source* package ‘ddalpha’ ...

** package ‘ddalpha’ successfully unpacked and MD5 sums checked

** libs

clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c AlphaProcedure.cpp -o AlphaProcedure.o

clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c Common.cpp -o Common.o

clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c DKnn.cpp -o DKnn.o

clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c HD.cpp -o HD.o

HD.cpp:25:14: warning: unused variable 'eps_Cmb1' [-Wunused-const-variable]

const double eps_Cmb1 = 1e-8;

             ^

1 warning generated.

clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c Knn.cpp -o Knn.o

Knn.cpp:146:15: warning: unused variable 'd' [-Wunused-variable]

        unsigned int d = points[0].size();unsigned int n = points.size();

                     ^

Knn.cpp:209:15: warning: unused variable 'd' [-Wunused-variable]

        unsigned int d = points[0].size();

                     ^

2 warnings generated.

clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c Mahalanobis.cpp -o Mahalanobis.o

Mahalanobis.cpp:32:6: warning: unused variable 'res' [-Wunused-variable]

        int res = lu_factorize(A, pm);

            ^

1 warning generated.

clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c OjaDepth.cpp -o OjaDepth.o

OjaDepth.cpp:44:8: warning: unused variable 'sc' [-Wunused-variable]

                bool sc = numSimplicesChecked == div0;

                     ^

1 warning generated.

clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c Polynomial.cpp -o Polynomial.o

Polynomial.cpp:396:18: warning: unused variable 'tmp' [-Wunused-variable]

        for (int i = 0, tmp; i < numPoints; i++){ input2[i][0] = input[i][1]; input2[i][1] = input[i][0]; } // swap columns

                        ^

1 warning generated.

clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c PotentialDepth.cpp -o PotentialDepth.o

clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c ProjectionDepth.cpp -o ProjectionDepth.o

ProjectionDepth.cpp:16:12: warning: unused function 'CompareAsc' [-Wunused-function]

static int CompareAsc(OrderRec x, OrderRec y)

           ^

ProjectionDepth.cpp:21:12: warning: unused function 'CompareDec' [-Wunused-function]

static int CompareDec(OrderRec x, OrderRec y)

           ^

2 warnings generated.

clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c SimplicialDepth.cpp -o SimplicialDepth.o

SimplicialDepth.cpp:46:8: warning: unused variable 'sc' [-Wunused-variable]

                bool sc = numSimplicesChecked == div0;

                     ^

1 warning generated.

clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c TukeyDepth.cpp -o TukeyDepth.o

clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c ZonoidDepth.cpp -o ZonoidDepth.o

ZonoidDepth.cpp:63:25: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]

    if ( RowInverted[j] = z[j] < 0 ) {

         ~~~~~~~~~~~~~~~^~~~~~~~~~

ZonoidDepth.cpp:63:25: note: place parentheses around the assignment to silence this warning

    if ( RowInverted[j] = z[j] < 0 ) {

                        ^

         (                        )

ZonoidDepth.cpp:63:25: note: use '==' to turn this assignment into an equality comparison

    if ( RowInverted[j] = z[j] < 0 ) {

                        ^

                        ==

1 warning generated.

clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c asa047.cpp -o asa047.o

clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c ddalpha.cpp -o ddalpha.o

gfortran   -fPIC  -g -O2  -c depth.fd.f -o depth.fd.o

make: gfortran: No such file or directory

make: *** [depth.fd.o] Error 1

ERROR: compilation failed for package ‘ddalpha’

* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/ddalpha’

 

The downloaded source packages are in

‘/private/tmp/RtmpUg5Cs2/downloaded_packages’

Warning message:

In install.packages(c("ddalpha", "recipes")) :

  installation of package ‘ddalpha’ had non-zero exit status

> 

]]> Jit https://bioinformaticsonline.com/answers/view/35388/how-to-extract-all-the-reads-mapped-at-specific-region-in-a-genome Mon, 29 Jan 2018 08:12:21 -0600 https://bioinformaticsonline.com/answers/view/35388/how-to-extract-all-the-reads-mapped-at-specific-region-in-a-genome <![CDATA[How to extract all the reads mapped at specific region in a genome?]]>  I want to extract all the reads mapped at chr5: 200-6000. 

]]> Poonam Mahapatra https://bioinformaticsonline.com/answers/view/35259/%CE%B4%CE%B4g-value-in-i-mutant-and-istable-server Thu, 18 Jan 2018 04:10:08 -0600 https://bioinformaticsonline.com/answers/view/35259/%CE%B4%CE%B4g-value-in-i-mutant-and-istable-server <![CDATA[ΔΔG value in I-mutant and iStable server]]> what may be the cause that ΔΔG value in I-mutant and iStable server different for same mutation, when the predictor for iStable is I-mutant?

I-mutant ΔΔG value is -2.12

iStable ΔΔG value is -1.47

]]> Andaleeb https://bioinformaticsonline.com/answers/view/35179/where-to-put-my-ssh-keys Mon, 15 Jan 2018 07:58:45 -0600 https://bioinformaticsonline.com/answers/view/35179/where-to-put-my-ssh-keys <![CDATA[Where to put my SSH keys?]]> Neel https://bioinformaticsonline.com/answers/view/35069/can-anyone-please-suggest-a-read-simulator-with-ngs-flexibly Sat, 06 Jan 2018 12:24:18 -0600 https://bioinformaticsonline.com/answers/view/35069/can-anyone-please-suggest-a-read-simulator-with-ngs-flexibly <![CDATA[Can anyone please suggest a read simulator with NGS flexibly ?]]> Neel https://bioinformaticsonline.com/answers/view/34924/what-are-the-difference-between-synteny-and-collinearity-terms Thu, 28 Dec 2017 09:17:50 -0600 https://bioinformaticsonline.com/answers/view/34924/what-are-the-difference-between-synteny-and-collinearity-terms <![CDATA[What are the difference between Synteny and Collinearity terms?]]> I sometime got confused with Synteny and Collinearity terminology. I am still wondering about the major differences.

]]> Rahul Nayak