Hello All,
I've been trying to use the FASTX Toolkit barcode splitter to demultiplex my illumina reads. The following command runs okay without any errors:
[cat /home/johnathon/jda_ev_extended.txt | fastx_barcode_splitter.pl --bcfile /home/johnathon/mybarcodes.txt --bol --mismatches 1 --prefix /home/johnathon/split_bc/jda_ev_split_bc --suffix ".txt"]
But none of the output files contain any reads except for the mismatched file.
The following is mybarcode.txt file:
[#I hope the following is the appropriate format for this txt file, it should contain the barcode identifier and the barcode sequence itself in a tab delimited fashion--Johnathon David Anderson
BC1 ACCC
BC2 CGTA
BC3 GAGT
BC4 TTAG]
However, when I look at the extended.txt file i can see the right barcodes on the 5' end. I have also tried to use the export.txt file to no avail; apparently it is not formatted appropriately. I get an error message saying for the first character there is an "S" instead of an "<" or an "@".
I have not converted these files from Solexa to Sanger Fastq. Could this be the issue?
For my first data set that was not barcoded I was using the MAQ fq_all2std.pl script export2std command to convert the export.txt file. It worked just fine and I was able to visualize the data on IGV. I haven't had much success with MAQ patch ill2sanger and am wondering if this is the issue with FASTX Toolkit, then can anyone recommend a user friendly script to convert. I am using Solexa pipeline 1.6.
Is anyone familiar with the FASTX Toolkit? Is the problem probably that the Illumina files need to be converted to Sanger FASTQ first?
Any guidance would be most appreciated?
Regards,
Johnathon
I've been trying to use the FASTX Toolkit barcode splitter to demultiplex my illumina reads. The following command runs okay without any errors:
[cat /home/johnathon/jda_ev_extended.txt | fastx_barcode_splitter.pl --bcfile /home/johnathon/mybarcodes.txt --bol --mismatches 1 --prefix /home/johnathon/split_bc/jda_ev_split_bc --suffix ".txt"]
But none of the output files contain any reads except for the mismatched file.
The following is mybarcode.txt file:
[#I hope the following is the appropriate format for this txt file, it should contain the barcode identifier and the barcode sequence itself in a tab delimited fashion--Johnathon David Anderson
BC1 ACCC
BC2 CGTA
BC3 GAGT
BC4 TTAG]
However, when I look at the extended.txt file i can see the right barcodes on the 5' end. I have also tried to use the export.txt file to no avail; apparently it is not formatted appropriately. I get an error message saying for the first character there is an "S" instead of an "<" or an "@".
I have not converted these files from Solexa to Sanger Fastq. Could this be the issue?
For my first data set that was not barcoded I was using the MAQ fq_all2std.pl script export2std command to convert the export.txt file. It worked just fine and I was able to visualize the data on IGV. I haven't had much success with MAQ patch ill2sanger and am wondering if this is the issue with FASTX Toolkit, then can anyone recommend a user friendly script to convert. I am using Solexa pipeline 1.6.
Is anyone familiar with the FASTX Toolkit? Is the problem probably that the Illumina files need to be converted to Sanger FASTQ first?
Any guidance would be most appreciated?
Regards,
Johnathon
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