Hello, I need some help.
I have to use droptag on 2 fastq.gz files (an internship assigned work) coming from here
I want to use the droptag utility in order to demultiplex my fastq.gz files (as it extracts the cell barcodes and UMIs from the library): the syntax is like this:
droptag [options] -c config.xml barcode_reads.fastq [barcode_umi_reads.fastq] gene_reads.fastq [library_tags.fastq]
But, droptag needs a .fastq barcode files and all I have are 3 .txt files with the barcodes of the 3 rounds of SPLIT-seq barcoding:
Their format is like this:
For Round1 and 2:
#WellPosition Name Sequence A1 Round1_01 /5Phos/CGCGCTGCATACTTGAACGTGATCCCATGATCGTCCGA A2 Round1_02 /5Phos/CGCGCTGCATACTTGAAACATCGCCCATGATCGTCCGA A3 Round1_03 /5Phos/CGCGCTGCATACTTGATGCCTAACCCATGATCGTCCGA A4 Round1_04 /5Phos/CGCGCTGCATACTTGAGTGGTCACCCATGATCGTCCGA
#WellPosition Name Sequence A1 Round3_01 /5Biosg/CAGACGTGTGCTCTTCCGATCTNNNNNNNNNNAACGTGATGTGGCCGATGTTTCG A2 Round3_02 /5Biosg/CAGACGTGTGCTCTTCCGATCTNNNNNNNNNNAAACATCGGTGGCCGATGTTTCG A3 Round3_03 /5Biosg/CAGACGTGTGCTCTTCCGATCTNNNNNNNNNNATGCCTAAGTGGCCGATGTTTCG
I don't know what to do, do I have to write a script? I don't even know for now what a barcode.fastq file should look like.
Or is there already an utility that solves this problem? I looked on the web but didn't find anything promising.
And yes, I tried, droptag doesn't work with .txt files.