Question: Matching list of barcodes to specific bases to read2 in a paired end file
0
gravatar for bibaswan.ghoshal
12 weeks ago by
bibaswan.ghoshal0 wrote:

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.

ADD COMMENTlink written 12 weeks ago by bibaswan.ghoshal0

example of input / output is needed.

ADD REPLYlink written 12 weeks ago by Pierre Lindenbaum115k

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

ADD REPLYlink modified 12 weeks ago by Pierre Lindenbaum115k • written 12 weeks ago by bibaswan.ghoshal0
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