search

YiPeng-Gao / scDaPars

Dynamic Analysis of Alternative Polyadenylation from single-cell RNA-seq (scDaPars)
10 stars 1 forks source link

the number of bam for single cell #17

Open yangfeizZZ opened 2 years ago

yangfeizZZ commented 2 years ago

Hi I have a bam about 40G.I creat the bam for single cell about 60000.The number is so large.could you tell me your number of bam for single cell.If possiable ,would you mind providing your code for me .Thank you very much Yang Fei 2021.9.24

YiPeng-Gao commented 2 years ago

I dont know how much single cell your Bam would have. you should be able to find that information where you download your dataset. Only open as many single cell bam files as the number of single cells. Then the reads will be assigned to different cells based on their cell barcode "CB" TAG in the bam file.

yangfeizZZ commented 2 years ago

This is my flow path.Could you please tell me the error. FilterBam INPUT=possorted_genome_bam.bam OUTPUT=possorted_genome_bam.filter.bam samtools sort possorted_genome_bam.filter.bam -o possorted_genome_bam.sort.filter.bam samtools index possorted_genome_bam.sort.filter.bam umi_tools dedup -I possorted_genome_bam.sort.filter.bam -S possorted_genome_bam.deduplicated.bam -- \ method=unique --extract-umi-method=tag --umi-tag=UB --cell-tag=CBsamtools sort -t CB possorted_genome_bam.deduplicated.bam -o pos_sort_tag.bam python delsam9.py input output