ChangqingW
ChangqingW
Hi, the match_cell_barcode binary file was outdated. `barcode match` should read `fuzzy match`. I added some description to match_cell_barcode [here](https://github.com/ChangqingW/FLAMES/commit/11615ed33914c2c74e2ef7e07c4c6c0e250ac73f). The “Barcode hm match” count includes both exact matches and...
could you run ``` /Software/anaconda_py2/bin/minimap2 -ax splice -t 12 --junc-bed FLAMES_Output/test/tmp.splice_anno.bed12 --junc-bonus 1 -k14 --secondary=no hg38v99.Cellranger.genome.fa test.demultiplexed.fq.gz | samtools view -bS -@ 4 -m 2G -o FLAMES_Output/test/tmp.align.bam - ``` and...
Please try out my `custom.css`, see #101 .
Allowing a maximum edit distance as specified for the `` argument in `match_cell_barcode`. Both flanking sequence alignment and barcode matching allow up to ``.
I believe it is currently implemented as "for each"
Yes, it is expecting fastq files outputted by match_cell_barcode, where the identifier field has the format of `@[barcode]_[umi]#[original id]`
> But this fastq file couldn't be viewed by `less`, it's a biniary file. And it couldn't be aligned with `minimap2` either, here is the error log: > > ```...
seems like ggplot2 is complaining `group.selfish` being passed to `layer`
Not sure if this is relevant, but using `rowRanges()
In case anyone else encountered the same error, it is probably secondary alignments missing sequences, skipping them in pileup might help: ``` Rsamtools::pileup(bam, scanBamParam = Rsamtools::ScanBamParam(flag = Rsamtools::scanBamFlag(isSecondaryAlignment = FALSE)))...