AfshinLab / BLR

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Integrate stLFR type reads #6

Closed pontushojer closed 4 years ago

pontushojer commented 4 years ago

Relates for issue https://github.com/FrickTobias/BLR/issues/204.

Integrate stLFR

The PR integrates stLFR type reads into the pipeline. Note that I could not find any unprocessed FASTQ files. All stLFR data has been demultiplexed using the the tool stLFR_read_demux. This removes the combinatorial barcode from the reads and translates it into a three-part index (e.g. #12_54_93) which is appended to the header of the read.

The processing to integrate into the BLR pipeline is in two steps. First a trim of any possible 3' adaptor (from tagmentation) using cutadapt and then translation of the three-part index into a three-part barcode using blr process_stlfr. The translation is made using a barcode whitelist file from the stLFR_read_demux tool. The process_stlfr script also modifies the headers to work with downstream processing (e.g different mappers and tagbam).

pontushojer commented 4 years ago

As there are seem to be no objections on this PR I will go ahead and merge it.