barcode analysis

[cnicolet]

Hello:
Does anyone have a clever (ie, one step) way of doing ELAND alignments on reads with 5' index sequences while maintaining the index sequence info for each individual read? The only ways I've heard about involve re-analyzing, either from images using a custom runinfo.xml file, or splitting the reads by index sequence then re-aligning with those sequences removed. I'm too lazy for that!

CN

[cbrennan]

Are you using pipeline v1.5.1? if so after you run eland you can run the split_on_index.py script and it will bin your results by barcode.

The script needs an .xml sheet that tells it what barcodes to look for in each lane. The usage text for the script will tell you the format of the xml file expected.

[cnicolet]

Thanks! I will look into that. But you're still not getting alignment info, are you?

[cbrennan]

It should parse out the eland info and give you alignment stats for each barcode.