Hello,
I've received a data set of old Illumina PE data. (R1, R2, R3).
Paired end files are R1 and R3.
I've split R1 and R3 into sample barcodes with fastx_barcode_splitter.
Then I proceeded to remove MIP arms with cutadapt.
After barcode split the reads in fastq files I'm getting are not even in both R1 and R3. So I can't align with bwa or bowtie2..
Fastx is messing files, is there any way to keep common reads in both PE or other tool to separate fastq by barcodes?
Maybe I should try removing MIP arms first then splitting into barcodes.. but I think the result is gonna be the same.
I've received a data set of old Illumina PE data. (R1, R2, R3).
Paired end files are R1 and R3.
I've split R1 and R3 into sample barcodes with fastx_barcode_splitter.
Then I proceeded to remove MIP arms with cutadapt.
After barcode split the reads in fastq files I'm getting are not even in both R1 and R3. So I can't align with bwa or bowtie2..
Fastx is messing files, is there any way to keep common reads in both PE or other tool to separate fastq by barcodes?
Maybe I should try removing MIP arms first then splitting into barcodes.. but I think the result is gonna be the same.
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