User: sjneph

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sjneph600
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Posts by sjneph

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Comment: C: Bed File Of Mapq Sliding Window On A Bam File?
... updated to put MAPQ in field 5 of your-file.bed since that's what you want to average over. ...
written 4.8 years ago by sjneph600
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Answer: A: Bed File Of Mapq Sliding Window On A Bam File?
... 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 4.8 years ago by sjneph600
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Answer: A: Where To Find Encode Dnase I Footprint Data
... 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 4.8 years ago by sjneph600
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Answer: A: Split Bed File To Another Bed Files With Specific Cordinates
... 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 4.8 years ago by sjneph600
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Answer: A: Separate Bed File To Each 60Kb Bins
... Here is a straightforward way to do it with awk: A: Does bedops have a command similar to the bedtools makewindows? ...
written 4.8 years ago by sjneph600
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Answer: A: Is It Possible To Filter Only Bookend Reads From A Bed File?
... 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 4.9 years ago by sjneph600
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Answer: A: Output The Overlapping Regions To New File
... 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 4.9 years ago by sjneph600 • updated 4.9 years ago by Alex Reynolds26k
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Answer: A: How Can I Include One Bed File In Another Bed File ?
... 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 5.3 years ago by sjneph600
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Answer: A: Split A Bam File Into Several Files Containing All The Alignments For X Number O
... 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 5.6 years ago by sjneph600
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Comment: C: What Are The Most Common Stupid Mistakes In Bioinformatics?
... 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 5.6 years ago by sjneph600

Latest awards to sjneph

Supporter 4.7 years ago, voted at least 25 times.
Teacher 4.8 years ago, created an answer with at least 3 up-votes. For A: Where To Find Encode Dnase I Footprint Data
Teacher 5.8 years ago, created an answer with at least 3 up-votes. For A: Manipulating Wiggle Files
Teacher 5.8 years ago, created an answer with at least 3 up-votes. For A: Comparing 2 Large Lists (Millions Of Rows) To Identify Shared And Exclusive Elem
Good Answer 5.8 years ago, created an answer that was upvoted at least 5 times. For A: Comparing 2 Large Lists (Millions Of Rows) To Identify Shared And Exclusive Elem
Teacher 5.8 years ago, created an answer with at least 3 up-votes. For A: Group Reads In Bed File Based On The Distance
Commentator 5.9 years ago, created a comment with at least 3 up-votes. For C: Bedtools: Analyzing Genomic Features
Teacher 5.9 years ago, created an answer with at least 3 up-votes. For A: Does Bedops Have A Command Similar To The Bedtools Makewindows?

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