No match to barcodes

[Rahmmy]

Hello,
I really enjoy the workflow of barseq as it seems to do exactly what I want. Unfortunately anytime I attempt using it I get 100% of my reads not having the barcodes. However, when I use a simple grep command I find the barcodes. Do I need to format my barcodes in a particular way before input?

[eburgoswisc]

Hi Rahmmy,
I am currently working on an update that will allow you to provide the left and right flanking sequences and match the barcode in the middle. We will also include an option that allows you to change the length of the barcode you want to match.

[eburgoswisc]

Hi Rahmmy,

there is a version of barseq here where you can change the flanking sequences and length of the barcode you are searching.

-fr FLANKING_RIGHT, --flanking-right FLANKING_RIGHT
-fl FLANKING_LEFT,  --flanking-left FLANKING_LEFT
--barcode-length BARCODE_LENGTH
                        Length of barcode sequence

If you did not provide a file with barcode sequences, there is also a --reference-free mode that will infer the 'good' barcodes in the sample files. Let me know if this helps.