scaff_BC-reads-2 parameter order
The genome assembly pipeline based on read clustering
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#1 scaff_BC-reads-2 parameter order
Are the parameters in 'scaff_BC-reads-2' in the wrong order?
./scaff_BC-reads-1
Usage: scaff_BC-reads-1 <input read_1 file <output read_1="" file=""> <output name_1="" file=""></output></output>
./scaff_BC-reads-2
Usage: scaff_BC-reads-2 <input name_1="" file=""> <input read_2 file > <out read_2="" file=""> </out>
It seems strange and very counter-intuitive that the 10x fastq file would be placed first in scaff_BC-reads-1 and second in scaff_BC-reads-2
Dear Colleague,
Many thanks for your interests in Scaff10x.
Say you have two fastq files from 10x platform:
read_1.fastq
read_2.fastq
You convert the fastq files first:
/nfs/users/nfs_z/zn1/src/scaff10x/scaff_BC-reads-1
read_1.fastq read-BC_1.fastq read-BC_1.name > try.out
/nfs/users/nfs_z/zn1/src/scaff10x/scaff_BC-reads-2
read-BC_1.name read_2.fastq read-BC_2.fastq > try.out
Here scaff_BC-reads-1 does
(1) extract the fist 16 barcode bases from read 1 and append to read names
Note the read name here contains the barcode tag
(2) write a file contains all the read names for use in the R2 file
Input: read_1.fastq
Output: read-BC_1.fastq read-BC_1.name
scaff_BC-reads-2
(1) Inputs read-BC_1.name and read_2.fastq
(2) Outputs the file read-BC_2.fastq
You need to cat all the BC_1.fastq file and BC_2.fastq files if you habe
more than one pair.
Hope it helps.
Zemin Ning
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Ah, got you! . Sorry, I'd not properly understood that it was a two-step process. Makes perfect sense with your explaination.
Thanks.