Illumina - Paired End Barcode Split + Mip trimmer

[gmarco]

Hello,

I've received a data set of old Illumina PE data. (R1, R2, R3).

Paired end files are R1 and R3.

I've split R1 and R3 into sample barcodes with fastx_barcode_splitter.
Then I proceeded to remove MIP arms with cutadapt.

After barcode split the reads in fastq files I'm getting are not even in both R1 and R3. So I can't align with bwa or bowtie2..

Fastx is messing files, is there any way to keep common reads in both PE or other tool to separate fastq by barcodes?

Maybe I should try removing MIP arms first then splitting into barcodes.. but I think the result is gonna be the same.

[relipmoc]

You may try flexbar and/or skewer. Or if you send of part of your data to me, I can analyze for you, then tell you how to do.

[JackieBadger]

if you do not care about insert size information then you can just put your paired ends into one file and align in single end mode

[gmarco]

I cannot send this data (it's private). But i'm gonna try with flexbar and skewer.
I'll report asap.

[gringer]

I cannot send this data (it's private).

FWIW, there's a very good chance that there exists freely available public data in the same format. Get some help working with the public data, and you'll be most of the way in dealing with your private data.

[gmarco]

FWIW, there's a very good chance that there exists freely available public data in the same format. Get some help working with the public data, and you'll be most of the way in dealing with your private data.

Totally agree. Next time I'll test with public data so I can get better help.
Flexbar is processing reads atm, it seems that's ok. Anyways I'll report when process is done.

BC split went perfectly.
Now I'm removing adapters with flexbar too. Let's see how it goes..