Comments (1)
No I don't have it explicitly documented anywhere.
- qname: query name of the original read
- sc_q_scores: phred-scaled base quality scores of the soft-clipped sequence
- sc_seq: nucleotide sequence of the soft-clipped sequence
- sc_avg_bq: average base quality of soft-clipped sequence
- avg_bq: average base quality of the entire read
- art_status: boolean value specifying whether this soft-clip was identified as artifact or not
As far as a histogram goes, I think creating the histogram could be done with bash tools.
This line below should extract the lengths of all the soft-clipped sequences from fade's stats-clip output:
cat fade_stats_clip_output.tsv | cut -f3 | awk '{ print length }' > soft_clipped.lengths.txt
Then by following this stack overflow question: https://stackoverflow.com/questions/39614454/creating-histograms-in-bash
If you save their script to the file hist.sh
(I would also modify the bin size to be something like 3bp):
chmod +x hist.sh
./hist.sh soft_clipped.lengths.txt
That could output what you need. It should output a column of bins and a column of bin sizes.
Though I haven't tested this yet. I could add a histogram-clips
subcommand to fade, though it would yield similar results. If you would like to plot a histogram, that would be outside of fade's scope, but the stats-clip
output has the data you need. Let me know if that helps at all.
from fade.
Related Issues (20)
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from fade.