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How to demultiplex csfasta files

I have a csfasta file (+the corresponding qual file) which contains color-space reads from different experiments which were multiplexed using different barcodes (4 nucleotides at the 5' end of the F3 read). Is there a tool to demultiplex these different experiments, similar to the fastx_barcode_splitter, but which works with csfasta files, not fastq?

chip-seq next-gen
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updated by Ram Ram • written by r.chereji • r.chereji

Reopened per user feedback.

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written by Dan D Dan D

The previous post is 4 years old and doesn't have any solution, so I think it is worthless waiting for someone else to post a solution there...

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written by r.chereji • r.chereji

1 answer

The solid platform is unsupported and the tools are mostly gone. I would recommend transforming your reads into letterspace with the so called double encoding 0->A, 1->T, 2->C, 3->G then use a barcode splitter for letter space to demultiplex, then transform back to colorspace

Some scripting will be required.

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written by Istvan Albert Istvan Albert

Thank you for the answer. I thought there are some tools available which demultiplex the experiments directly, especially because the Pugh lab deposit most of their data on SRA database in this form (multiplexed color-space reads), and I expected that there are also well known tools which one could use to obtain the data from individual experiments, remove the barcodes, etc.

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updated by Ram Ram • written by r.chereji • r.chereji

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