Hi, I need your help because I'm completely lost with that. I received a paired-end sequencing containing many samples in a forward and reverse paired end fastq set of files as shown below.
I was expecting to find a software that could extract the samples in a way similar as shown below, not because is just a personal plan but because is commonly used in some softwares (qiime is an example).
##  "PN1R1_L001_R1_001.fastq" "PN1R1_L001_R2_001.fastq" ##  "PN3R2_L001_R1_001.fastq" "PN3R2_L001_R2_001.fastq"
My problem started when I figured out that some of those samples share the forward barcode, but the difference is in the reverse one, and I´ve never seen something like that. I assume is a feature of modern sequencing platforms with high capacities and with the propper sofware those could be easily splitted and assign to propper derived fastq files.
Sample Espacer Forward Espacer Reverse 1 PN1R1 A B 2 PN3R1 A C 3 PN1R2 B C 4 PN3R2 B D
As you can see, the forward A is contained in two samples, but those doesn´t have the same reverse barcode. As example of the files, show that contain a barcode that can be in the forward and the reverse, an index doing a difference and the forward and reverse primer.
SAMPLE BARCODE INDEX SPECIFIC PRIMER For_A FORWARD CCTAAACTACGG CCTACGGGNGGCWGCAG For_B FORWARD TGCAGATCCAAC T CCTACGGGNGGCWGCAG Rev_B REVERSE TGCAGATCCAAC A GACTACHVGGGTATCTAATCC Rev_C REVERSE CCATCACATAGG TC GACTACHVGGGTATCTAATCC Rev_D REVERSE GTGGTATGGGAG CTA GACTACHVGGGTATCTAATCC
What I need is to find a sofware that could pick the samples acording to their respective barcodes, even if those are shared in some side and separate between samples. I've been trying some softwares (qiime1, fastx, mothur) but nothing worked as expected. Also I wanted to check qiime2 and SeekDeep too, but at this point I don´t want to waste time checking each software without having a real idea of what they can do.
Does somebody know that kind of post processing and give me a tip of a program which does that kind of job? I would be totally grateful for any hint.
Sorry for this large post but I just wanted to give as much details as I could. Thanks for your time