FADE Software References
References: Characterization and mitigation of double-strand artifacts induced by fragmentation enzymes -
Misidentification and removal software generated by enzyme digestion provided by PMC (nih.gov) literature FADE: Software git address
Literature Supplementary Material Figure: The base quality value of the artificial error sequence generated by enzyme digestion is relatively high, compared to the quality value of other softclips.
FADE software download
Download the linux versionFADE
wget https://github.com/blachlylab/fade/releases/download/v0.6.0/fade.many-linux-x86_64.tar.gz
software use
./fade annotate ${yourbam} > anno.bam # 先增加bam注释
./fade stats anno.bam > stats.out # 统计是否是artifact softclip(包含比对信息）
./fade stats-clip anno.bam > stats-clip.out # 统计是否是artifact softclip（质量值和是否是artifact)
stats-clip.outExample result file:
| qname | sc_q_scores | sc_seq | sc_avg_bq | avg_bq | art_status |
|---|---|---|---|---|---|
| A1:2:3:4 | F,FF,:F:F,FFFFFFF | TCGGGCCGGTCGTCTTT | 31.4444 | 31.8671 | false |
| A1:2:3:5 | F,FF,:F:F,FFFF::F:FF:F | TCGGGTTCGTGACCTCAGCGGC | 31.4444 | 31.8671 | ture |
Description of each column:
| header name | illustrate |
|---|---|
| qname | read name |
| sc_q_scores | softclip sequence quality value |
| sc_seq | softclip sequence |
| sc_avg_bq | softclip sequence quality value mean |
| avg_bq | The mean of the quality value of the sequence |
| art_status | Whether softclip is artifact [value: true/false] |
Learn more about:
Enzyme digestion and fragmentation library construction, strange knowledge increased
Enzyme Digestion Library Construction Kit v2 upgrade version is coming
** Fusion gene detection in FFPE samples: DNA or RNA
Comparison of Sonication Method and Enzyme Digestion Method for Random Genome Fragmentation