Dear all
I am new in this field. in need more clarified information about configuration file contents.
in the manual: "Parameters for the bowtie2, mateAn,
nucmer, asseMerge, and meta2fasta programs can be specified"
is that mean some parameters of all of these programs should specified mandatory or few of them depending on the purpuse or data that i have ?
for example i have A assemly (bowtie2 aligned PE illumina sequencing reads to pacbio long read sequence assembly and improved by pilon) and B assemly (ABySS assebly).
bott assemly around 35mb size.
i want to merge this two assembly. if it possible can you provide a example configurarion file and some recomendation to parameter selection ?
in brief i am bit confused at parameter and programs in configuration file.
Thanks in advance
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
You can find an example configuration file on the root directory of the
package ("Config1"). Regarding the parameters for external programs, the
mandatory bowtie parameters are:
Please refer to the corresponding manual to find out about these. Also, it
is recommended that you set the nucmer parameters:
nucmer_l=<int>
nucmer_c=<int>
Again, please refer to the corresponding manual. These will regulate the
interplay between the accuracy of Whole Genome Alignments and the
computation load of this stage.
Dear all
I am new in this field. in need more clarified information about
configuration file contents.
in the manual: "Parameters for the bowtie2, mateAn,
nucmer, asseMerge, and meta2fasta programs can be specified"
is that mean some parameters of all of these programs should specified
mandatory or few of them depending on the purpuse or data that i have ?
for example i have A assemly (bowtie2 aligned PE illumina sequencing reads
to pacbio long read sequence assembly and improved by pilon) and B assemly
(ABySS assebly).
bott assemly around 35mb size.
i want to merge this two assembly. if it possible can you provide a
example configurarion file and some recomendation to parameter selection ?
in brief i am bit confused at parameter and programs in configuration
file.
Dear all
I am new in this field. in need more clarified information about configuration file contents.
in the manual: "Parameters for the bowtie2, mateAn,
nucmer, asseMerge, and meta2fasta programs can be specified"
is that mean some parameters of all of these programs should specified mandatory or few of them depending on the purpuse or data that i have ?
for example i have A assemly (bowtie2 aligned PE illumina sequencing reads to pacbio long read sequence assembly and improved by pilon) and B assemly (ABySS assebly).
bott assemly around 35mb size.
i want to merge this two assembly. if it possible can you provide a example configurarion file and some recomendation to parameter selection ?
in brief i am bit confused at parameter and programs in configuration file.
Thanks in advance
Hi,
You can find an example configuration file on the root directory of the
package ("Config1"). Regarding the parameters for external programs, the
mandatory bowtie parameters are:
bowtie2_read1=<path1>[,...,<pathN>]
bowtie2_read2=<path1>[,...,<pathN>]
bowtie2_maxins=<int>
bowtie2_minins=<int>
Please refer to the corresponding manual to find out about these. Also, it
is recommended that you set the nucmer parameters:
nucmer_l=<int>
nucmer_c=<int>
Again, please refer to the corresponding manual. These will regulate the
interplay between the accuracy of Whole Genome Alignments and the
computation load of this stage.
Wences
On Wed, Aug 2, 2017 at 1:07 AM, Dava davaasuren1@users.sf.net wrote: