cemba_data

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cutadapt command in snakemake templates (for example [cemba_data/mapping/Snakefile_template/mc.Snakefile](https://github.com/lhqing/cemba_data/blob/master/cemba_data/mapping/Snakefile_template/mc.Snakefile)) has a bug # Trim reads rule trim_r1: input: "fastq/{cell_id}-R1.fq.gz" output: fq=temp("fastq/{cell_id}-R1.trimmed.fq.gz"), stats=temp("fastq/{cell_id}-R1.trimmed.stats.tsv") threads: 2 shell: "cutadapt --report=minimal -a {r1_adapter} {input} 2>...

mbatiuk

manual is outdated at https://hq-1.gitbook.io/mc Such as there is no mentioning about alternative to bismark hisat3n in the reference section: https://hq-1.gitbook.io/mc/prepare/prepare-mapping-config/prepare-reference-files However hisat3n is an option in the parameters for...

mbatiuk

potential error in yap make-sample-sheet plateinfo_and_samplesheet.py

1

https://github.com/lhqing/cemba_data/blob/788e83cd66f3b556bdfacf3485bed9500d381f23/cemba_data/demultiplex/plateinfo_and_samplesheet.py#L94 I changed `ll = re.split(r' |,|\t', 'line')` to `ll = re.split(r' |,|\t', line)` and `yap make-sample-sheet` works

MichaelPeibo

Thanks for sharing your data analysis pipeline There is an issue when performing read mapping using your pipeline After demultiplexing into cell level fastq, Snakefile is created in each multiplex...

mbatiuk

pipeline installation described here fails: https://hq-1.gitbook.io/mc/installation pip install allcools requires additional dependency libxcrypt performing mamba install libxcrypt solves the issue

mbatiuk

Hi I am trying to get the Methylome and transcriptome data from GSE14049 in single cell level, however I am running `yap default-mapping-config --barcode_version V1 --mode mct --bismark_ref ref/Bisulfite_Genome --genome_fasta...

TinaXiayanLi

nova x has 8 lanes

jksr

Good morning, I am encountering some errors while reprocessing single-cell level data downloaded from SRA. The issue is the way read names are split in the part devoted to contact...

GMFranceschini