how to split paired-end fastq by barcode from smart-seq2
i have a pooled fastq, it is paired-end sequencing, i wan to split fastq by barcode,which soft should i choose? thank you
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You can use my Genozip tool:
genozip myfile.fq.gz --fast
genocat --grep-w TTAGGC myfile.fq.genozip # output all reads with the barcode TTAGGC
If you also want to also properly compress the fastq file (1.5-2X better than gz) while you're at it, replace the first command with:
genozip myfile-R1.fq.gz myfile-R2.fq.gz --pair --reference hs37d5.ref.genozip
Where the reference file is generated from any FASTA reference genome of the species with eg:
genozip --make-reference hs37d5.fa
See here: https://genozip.com
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