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).
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 usingblr process_stlfr
. The translation is made using a barcode whitelist file from the stLFR_read_demux tool. Theprocess_stlfr
script also modifies the headers to work with downstream processing (e.g different mappers andtagbam
).