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Matching list of barcodes to specific bases to read2 in a paired end file

Hi,

I have a list of barcodes each 8nt long. I want to look for these barcodes in specific bases (11-18, 47-54, 89-96) of the read 2 sequences allowing 1 mismatch in each region and then filtering the reads that have these barcodes and then match them with the read 1.

I tried at multiple programs like cutadapt, barcode_splitter but they can't be able to handle the method? How can this be achieved?

Thanks for any help you can offer.

rna-seq scrnaseq split-seq barcode trimming
• 1,562 views • link
updated by Biostar Biostar • written by bibaswan.ghoshal • bibaswan.ghoshal

Input files: sample1_R1.fastq.gz

@NS500310:191:H3WFYBGX9:1:11101:10722:1034 1:N:0:GATCAG
TATTANAGTTGCTGCAGTTAAAAAGCTCNTAGTTGGATCTTGGGAGCGGGCGGGCGGTCCGCCGCG
+
AAAAA#EEEEEEEEEEEEEEEEEEEEEE#EEEEEEEEEEEEEEE/EEEEEEEEEEEEEEE<EAEE/
@NS500310:191:H3WFYBGX9:1:11101:9361:1035 1:N:0:GATCAG
GATTGNTTCTCAGTTGGACATGGTGGTGCAGGCCTGGTACTTGGAAGGTGTCCTAGGAGTCCTAGA
+
AAAAA#EEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEAAEA

sample1_R2.fastq.gz:

@NS500310:191:H3WFYBGX9:1:11101:10722:1034 2:N:0:GATCAG
NCGAGCAGNCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTGTAANCNNNNNNNNNNNNAGNNNANNNCNNTNNNATNCNNN
+
#/A/A//E#//########################################//A///#/############//###/###/##/###//#/###
@NS500310:191:H3WFYBGX9:1:11101:9361:1035 2:N:0:GATCAG
NTGCGTGTNTANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTCGAANCNNNNNNNNNNNNAGNNNAGNNCNNTCNNCCNCNNN
+
#AAAAEEE#A6########################################/6/E//#/############/A###/6##/##//##//#/###

barcodes.txt:

AACGTGAT
AAACATCG
ATGCCTAA
AGTGGTCA
ACCACTGT
ACATTGGC
CAGATCTG
CATCAAGT
CGCTGATC
ACAAGCTA

Desired output: Matched paired-end fastq

• 1 views • link
updated by Pierre Lindenbaum Pierre Lindenbaum • written by bibaswan.ghoshal • bibaswan.ghoshal

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