--error-correct-cell behaviour

Hi,

Thanks for the tool. I have a problem with --error-correct-cell, I don’t know if I misunderstood something.

So first I do a whitelist: umi_tools whitelist --extract-method=regex --bc-pattern='(?P<discard_1>TTCG){s<=1}(?P<cell_1>.{15,17})(?P<discard_2>TGCTTACGCTACGGAACGA){s<=3}(?P<umi_1>.{9})' --stdin=input.fastq -S BBC.txt Which give me in particular this line in the whitelist output file: CTGTTGATCACCCGTA CTGTTGATCACCCGTAT And then I do an extract: umi_tools extract --extract-method=regex --bc-pattern='(?P<discard_1>TTCG){s<=1}(?P<cell_1>.{15,17})(?P<discard_2>TGCTTACGCTACGGAACGA){s<=3}(?P<umi_1>.{9})' --whitelist BBC.txt --error-correct-cell --stdin=input.fastq -S input.BBC.fastq And in the output FASTQ file, I have this read header: @M05218:191:000000000-D7R5H:1:1102:14341:19429_CTGTTGATCACCCGTAT_CCTCAAACG 1:N:0:2 where I was expecting the BC to be corrected to “CTGTTGATCACCCGTA” but it actually has the uncorrect form (that was actually found in the read). Is it the expected behaviour? Did I misunderstand something?

Cheers, Mathieu

[TomSmithCGAT]

There is indeed a redundancy between --whitelist and --filter-cell-barcode, where the former is a path to a whitelist file and the later a switch to filter against this. We can leave this issue open as a reminder to remove the redundant option (suggest --whitelist to switch on --filter-cell-barcode and hide --filter-cell-barcode option to not break any users current pipelines). error-correct-cell is a separate option however since one might wish to only retain cells that perfectly match the whitelist

[mbahin]

Actually it looks like there is redundancy in the 3 options “–whitelist”, “-error-correct-cell” and “–filter-cell-barcode” no?