bamtofastq使用

10X单细胞数据如何从Bam转回Fastq

Posted by CHY on August 16, 2021

详细链接:https://support.10xgenomics.com/docs/bamtofastq

bamtofastq是10X官方专门开发的针对cellranger, cellranger-atac, cellranger-arc, cellranger-dna, spaceranger or longranger等软件生成的Bam倒推出fastq文件的工具。BAMs produced for TCR or BCR data, by aligning to a V(D)J reference with cellranger vdj or cellranger multi, are not supported by bamtofastq. Special tags是必须的,不然会报“WARNING: no @RG (read group) headers found in BAM file.”错误。所以从SRA下载的BAM文件也需要注意是否去除Tag。

/home/chenhy/software/bamtofastq-1.3.2 --nthreads=8 shr_root_mut_postsorted_genome_bam.bam