Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

scaled_bigwig takes fsize from picard #19

Merged
merged 3 commits into from
May 28, 2020
Merged

scaled_bigwig takes fsize from picard #19

Changes from 2 commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
a481c20
scaled_bigwig takes fsize from picard
May 22, 2020
c4e705c
Extract fragsize separated from scale_bigwig
May 25, 2020
be10592
Tidy up pull request
May 25, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
17 changes: 14 additions & 3 deletions Snakefile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -303,14 +303,25 @@ rule compute_scaling_factors:
with open(factor_path, "w") as f:
print(factor, file=f)

rule extract_fragment_size:
input:
insertsizes="restricted/{library}.insertsizes.txt"
output:
fragsize="restricted/{library}.fragsize.txt"
run:
with open(output.fragsize, "w") as f:
print(parse_insert_size_metrics(input.insertsizes)["median_insert_size"],
file=f)


rule scaled_bigwig:
output:
bw="scaled/{library}.scaled.bw"
input:
factor="factors/{library}.factor.txt",
fragsize="restricted/{library}.fragsize.txt",
bam="restricted/{library}.bam",
bai="restricted/{library}.bai",
bai="restricted/{library}.bai"
threads: 20
shell:
# TODO also run this
Expand All @@ -319,11 +330,11 @@ rule scaled_bigwig:
"bamCoverage"
" -p {threads}"
" --binSize 1"
" --extendReads"
" --extendReads $(< {input.fragsize})"
" --scaleFactor $(< {input.factor})"
" --bam {input.bam}"
" -o {output.bw}"


rule stats:
output:
Expand Down