本文へスキップ

Allpaths-lg

Allpaths-lg


allpaths-lg


Preparing ALLPATHS input files 

in_groups.csv
in_libs.csv
の2つのファイルを準備する。

例えば, in_groups.csvは,
 
group_name, library_name, file_name
302, Illumina_011, /seq/Illumina/011/302.bam
303, Illumina_012, /seq/Illumina/012/303.?.fasta
100, PacBio_007, /seq/PacBio/007/100.*.fastq.gz


もう一方は,in_libs.csv

library_name, project_name, organism_name, type, paired, ...
Illumina_011, Awesome, E.coli, fragment, 1, ...
Illumina_012, Awesome, E.coli, jumping, 1, ...
PacBio_007, Awesome, E.coli, long, 0, ...

... frag_size, frag_stddev, insert_size, insert_stddev, ...
... 180, 10, , , ...
... , , 3000, 500, ...
... , , , , ...

... read_orientation, genomic_start, genomic_end
... inward, ,
... outward, ,
... , ,

まず,PrepareAllPathsInputs.plでrunする。
inserted by FC2 system