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Hello,
I am trying to re-sync some illimina read files after phix filtering using your script but I am getting this error:

IOError: [Errno 2] No such file or directory: 'no_phix/T1-3-F_CGAGCGAC-TACGAGAC_L001_R1_001.fastq.gz.nophix.fastq.nophix.fastq_pairs_R1.fastq'
Traceback (most recent call last):
File "../fastqCombinePairedEnd.py", line 97, in
with myopen(in1 + "_pairs_R1" + outSuffix, "w") as out1:
File "../fastqCombinePairedEnd.py", line 66, in myopen
return open(infile, mode=mode)
IOError: [Errno 2] No such file or directory: 'no_phix/T4-1-C_CGAGCGAC-ACGTCTCG_L001_R1_001.fastq.gz.nophix.fastq.nophix.fastq_pairs_R1.fastq'
Traceback (most recent call last):
File "../fastqCombinePairedEnd.py", line 97, in
with myopen(in1 + "_pairs_R1" + outSuffix, "w") as out1:
File "../fastqCombinePairedEnd.py", line 66, in myopen
return open(infile, mode=mode)

Those are how the file names look like and are inside a folder called no_phix:
T1-3-F_CGAGCGAC-TACGAGAC_L001_R2_001.fastq.gz.nophix.fastq
T4-1-C_CGAGCGAC-ACGTCTCG_L001_R1_001.fastq.gz.nophix.fastq
T4-1-F_CGAGCGAC-GATCGTGT_L001_R1_001.fastq.gz.nophix.fastq
...

And this is my code:
ls no_phix/*nophix.fastq > fastq_nophix.list
cd no_phix
while read R1
do read R2
python ../fastqCombinePairedEnd.py $R1.nophix.fastq $R2.nophix.fastq
done < ../fastq_nophix.list

Thank you so much in advance,
G.

Hi

My headers look like this:
@NS500278:91:HK23CBGX2:2:13212:11182:16700/1
And
@NS500278:91:HK23CBGX2:1:11101:23209:1052/2

This is how I used the script:

python ResynchroniseFastq.py BAEL_R1_Final_Header.fastq BAEL_R2_Final_Header.fastq None

but every thing seems to be going in the singles file.

Am I doing something wrong?

Hello,

I'm trying to use your script to match two fastq files from an old illumina format (R1 and R3) (R2 contained barcodes).

I've already demultiplexed them with the barcodes on R2 and now I got my two fastq files (R1 and R3) with the sample names included.

My files look like this (4 lines per read), but I'm not sure if the header format it's ok for your script match paired reads on both files..

R1.fastq:
@sample1 MISEQ:154:000000000-A4PK2:1:2114:14962:29218 1:Y:0: orig_bc=CGTTAGCA new_bc=CGTTAGCA bc_diffs=0

R3.fastq:
@sample1 MISEQ:154:000000000-A4PK2:1:2114:14962:29218 3:Y:0: orig_bc=CGTTAGCA new_bc=CGTTAGCA bc_diffs=0

Apparently script is working. I've checked a few of the samples and seem to be well paired in both output files. But I would like if you can confirm me this.

Tried using the "fastqCombinePairedEnd.py" program. I received the following error (see below). Just thought I would forward it on to you.

File "fastqCombinePairedEnd.py", line 27
print doc
^
SyntaxError: Missing parentheses in call to 'print'