User: sjneph
sjneph • 600
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Posts by sjneph
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... updated to put MAPQ in field 5 of your-file.bed since that's what you want to average over.
...
written 5.3 years ago by
sjneph • 600
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...
bam2bed < your-file.bam | cut -f1-4,7 > your-file.bed
make-regions 1000 200 regions.bed | bedmap --echo --mean - your-file.bed > answer.bed
Where make-regions is an awk statement, perhaps buried in a shell script
awk -v winsize=$1 -v stepsize=$2 \
'{ \
i = $2; \
while ( i < $3 ) ...
written 5.3 years ago by
sjneph • 600
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... These are available through ftp at EBI.
As the README explains, all 41 cell type footprints are available in one file, and the FOS is shown in column 5 (lower score is a more significant score).
...
written 5.3 years ago by
sjneph • 600
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... Alex is spot on that you will receive a tremendous number of files that would be difficult to manage. Instead, you could consider demarcating every row with an indicator of what file it would be in with your method.
$ awk \
'{ \
regionChromosome = $1; \
regionStart = $2; \
...
written 5.3 years ago by
sjneph • 600
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... Here is a straightforward way to do it with awk:
A: Does bedops have a command similar to the bedtools makewindows?
...
written 5.3 years ago by
sjneph • 600
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... This is pretty straightforward with BEDOPS:
sort-bed file.bed > file.sort.bed
closest-features --no-overlaps --dist --closest file.sort.bed file.sort.bed | awk -F'|' '$3*$3==1'
You basically ask what elements are closest 'to the left' and 'to the right' of every element in the file using an ed ...
written 5.4 years ago by
sjneph • 600
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... sort-bed file1 > file1.sorted
sort-bed file2 > file2.sorted
bedops -e -1 file1.sorted file2.sorted > answer.bed
bedops -e -1 file2.sorted file1.sorted >> answer.bed
The answer.bed file will not be sorted per sort-bed since you catted on the results. If you want to maintain sort ...
written 5.4 years ago by
sjneph • 600
• updated
5.4 years ago by
Alex Reynolds ♦ 28k
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... use
bedops --merge a.bed b.bed > merged.bed
the requirements are that both bed files are sorted, which is easy and smart to do, as it makes all downstream analyses more efficient. The output is already sorted, so you only need to do this once for initial, unsorted files.
sort-bed A.bed > ...
written 5.9 years ago by
sjneph • 600
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... You might consider converting the bam file to starch format, which is a highly compressed version of BED. The starch file will be smaller than the original BAM file, and there is no loss of information. Once in starch format, you can use other BEDOPS utilities to annotate things the way you want. ...
written 6.1 years ago by
sjneph • 600
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31k
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... Yea, until you make the assumption that -w actually works only on whitespace.
printf "foo-choo" | grep -Fw -e "foo"
returns foo-choo. Hate that.
...
written 6.2 years ago by
sjneph • 600
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