Mapping BD Rhapsody Enhanced Beads

[Antidington]

Hello,

I referred to the method mentioned in #49 to construct the barcode whitelist for BD, but the parameters mentioned in that issue -x 0,0,9,0,21,30,0,43,52:0,52,60:1,0,0 seem to be for the BD v1 library. But in BD enhanced library, they changed the structure of the bead barcodes which complicates things a little bit. They have added staggered nucleotides (see below) at the start of the first barcode. This shifts the reads by several nucleotides to increase diversity and reduce the amount of PhiX needed, but it also complicates finding the barcodes based solely on base counting. Any ideas on how we could use kb to continue mapping these new types of CBs?

[Yenaled]

You will have to do an extra preprocessing step to search for the first barcode and reformat your reads so that the barcodes are at fixed position. That is the only way. You can try writing custom shell scripts or, if you're so inclined, try out our newest read preprocessing software to do so.

[Antidington]

You will have to do an extra preprocessing step to search for the first barcode and reformat your reads so that the barcodes are at fixed position. That is the only way. You can try writing custom shell scripts or, if you're so inclined, try out our newest read preprocessing software to do so.

Dear Yenaled,

I apologize for not replying in a timely manner and I greatly appreciate your patient answers. I have reconfirmed the library structure of BD, as shown in the picture. According to your suggestion, do I need to trim both the 3' and 5' reads to ensure the barcode is in a fixed position? Or do I only need to trim the 3' end data? I am not very clear about the specific alignment details of kb, so I need to confirm with you.

In addition, I am very willing to use splitcode to complete the above work. Could you please provide more information about this tool? For example, which function should I use to achieve my above requirements? Thank you very much!

Best regards,
Jichen