Integrated Isoform-Resolved Transcriptomic Analysis of Gossypium barbadense and Gossypium hirsutum Fibers

https://doi.org/10.1101/2024.10.11.617711

数据

subreads.bam 2 ccs.bam

  1. ccs \
  2.   *.subreads.bam \
  3.   ccs.bam \
  4.   --min-passes 0 \
  5.   --min-length 50 \
  6.   --max-length 21000 \
  7.   --min-rq 0.75 \
  8.   -j 4

比对

pbmm2

https://github.com/PacificBiosciences/pbmm2

  1. genome=
  2. sample=
  4. pbmm2 align \
  5.   --preset ISOSEQ \
  6.   --unmapped \
  7.   --sort \
  8.   -j 20 \
  9.   --log-level INFO \
  10.   --log-file pbmm2.log \
  11.   --sample ${sample} \
  12.   ${genome} \
  13.   ${sample}.bam
  1. bamtools stats -in ${sample}.bam > ${sample}.bam.stats

转录本组装

tama collapse

https://github.com/GenomeRIK/tama

  1. tama_collapse.py \
  2.   -d merge_dup \
  3.   -x no_cap \
  4.   -b BAM \
  5.   -f ${ref} \
  6.   -s ${sample}.bam \
  7.   -p ${sample} \
  8.   &> ${sample}.log

tama merge 多样本合并

isoform 过滤

参考

iso-seq

https://www.jianshu.com/p/c9434353b648

https://zhuanlan.zhihu.com/p/590003590

https://repost.aws/zh-Hans/knowledge-center/create-and-activate-aws-account