STAR 映射正在创建空 BAM 文件

Question

我正在尝试运行 STAR，但收到一个空的 BAM 文件。有谁知道为什么会发生这种情况以及如何解决它？

iCount mapstar demultiplexed/demux_NNNGGCGNN.fastq.gz hs88 mapping_NNNGGCGNN \
> --annotation homo_sapiens.88.gtf.gz 
#for context, mapstar needs the following arguments reads, genome_index, out_dir

iCount mapstar demultiplexed/demux_NNNGGCGNN.fastq.gz hs88 mapping_NNNGGCGNN --annotation homo_sapiens.88.gtf.gz
Input parameters for function 'map_reads' in iCount.externals.star
    reads: demultiplexed/demux_NNNGGCGNN.fastq.gz
    genome_index: hs88
    out_dir: mapping_NNNGGCGNN
    annotation: homo_sapiens.88.gtf.gz
    multimax: 10
    mismatches: 2
    threads: 1
    genome_load: False
Mapping reads from demultiplexed/demux_NNNGGCGNN.fastq.gz
Nov 02 20:23:11 ..... started STAR run
Nov 02 20:23:11 ..... loading genome
Nov 02 20:23:12 ..... processing annotations GTF
Nov 02 20:23:32 ..... inserting junctions into the genome indices
Nov 02 20:23:34 ..... started mapping
Done.

Answer 1

我通过将 --readFilesCommand zcat 替换为 --readFilesCommandgunzip -c 解决了这个问题