I used fastx_barcode_splitter.pl to demultiplex the barcodes to generate separate fastq files. However the files still retain the barcodes (at the beginning of each sequence in my case) . I want to remove those before the alignment.
First, is there an option in fastx_barcode_splitter.pl to remove the barcodes while splitting the file? if not, I tried using:
fastx_trimmer -f 5 -l 50 -i input.fastq -o output.fastq
it gives the following error:
fastx_trimmer: Invalid quality score value (char '#' ord 35 quality value -29) on line 4
I used python script python trimmer.py -f input.fastq -s 5 -e 50 > try.fastq
but it trims every line (not just the sequence line) leading to wrong fastq format.
please help.
thanks
First, is there an option in fastx_barcode_splitter.pl to remove the barcodes while splitting the file? if not, I tried using:
fastx_trimmer -f 5 -l 50 -i input.fastq -o output.fastq
it gives the following error:
fastx_trimmer: Invalid quality score value (char '#' ord 35 quality value -29) on line 4
I used python script python trimmer.py -f input.fastq -s 5 -e 50 > try.fastq
but it trims every line (not just the sequence line) leading to wrong fastq format.
please help.
thanks
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