Kallisto Pseudoalignment 작업 #

#2025-04-21

1. Build Index #

$ kallisto index -i transcripts_cDNA.idx Homo_sapiens.GRCh38.cdna.all.fa.gz

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2. Pseudoalign #

$ kallisto quant -i transcripts_cDNA.idx -o output_150-1 -t 40 ../2306_tophat/data/Bowtie2Index/5-AZA_150-1_1_edited.fastq ../2306_tophat/data/Bowtie2Index/5-AZA_150-1_2_edited.fastq

• 3개 파일 생성
  • abundance.h5 - HDF5 binary file containing run info, abundance esimates, bootstrap estimates, and transcript length information length. This file can be read in by sleuth
  • abundance.tsv - plaintext file of the abundance estimates. It does not contains bootstrap estimates. Please use the –plaintext mode to output plaintext abundance estimates. Alternatively, kallisto h5dump can be used to output an HDF5 file to plaintext. The first line contains a header for each column, including estimated counts, TPM, effective length.
  • run_info.json - json file containing information about the run

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3. Downstream 분석 #

• Kallisto는 일반적인 Alignment 도구와 달리 bam 파일을 output으로 생성하지 않기 때문에 HTSeq-count를 쓰는 대신 abundance.tsv 또는 .h5 파일을 Sleuth에서 직접 불러와서 통계 분석을 수행하는 것이 표준 워크플로우.

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