User: mujupas

gravatar for mujupas
mujupas40
Reputation:
40
Status:
New User
Location:
Japan
Last seen:
2 months ago
Joined:
4 years, 1 month ago
Email:
m******@hotmail.com

about me

Posts by mujupas

<prev • 18 results • page 1 of 2 • next >
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Comment: A: Bedtools subtract on a line-by-line basis
... Thanks a lot Alex, I'll try this out. Cheers! ...
written 9 weeks ago by mujupas40
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Bedtools subtract on a line-by-line basis
... Hi, is there a way to restrict the behaviour of bedtools to a line-by-line comparison? To be more clear, if I have 2 BED files: File_A: chr1 1 100 chr2 1 100 and File_B: chr2 50 70 chr3 1 100 I'd like bedtools subtract to eliminate from File_A the interval contained in one li ...
bedtools written 9 weeks ago by mujupas40
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GOseq enrichment test
... Hi! I have a list of bed intervals, some of which intersect with protein coding genes (Refseq). I'd like to use this Refseq genes list to run an enrichment test in GOseq, but I can't figure out how to skip the first steps of the standard GOseq workflow (given that I am not dealing with RNA-seq and ...
enrichment gene ontology goseq written 9 months ago by mujupas40
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Comment: C: Bedtools - Intervals frequency occurence in multiple files
... I'm very grateful for your help, thank you very much! ...
written 10 months ago by mujupas40
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Bedtools - Intervals frequency occurence in multiple files
... Hi! I have multiple BED files and I know that for each file some of the intervals are shared with some of the other files, while some are unique (for example present in one or 2 files only). Ideally, the final table should contain all the possible intervals with 2 columns, one for the count of fre ...
bedtools written 10 months ago by mujupas40 • updated 10 months ago by Alex Reynolds22k
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Comment: C: Replace BED intervals
... Worked like a charm, thank you so much! ...
written 3.1 years ago by mujupas40
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Comment: A: Replace BED intervals
... Thanks, it worked. The only problem is that now the new 1bp BED files are using spaces as separators and not TAB. I've tried the following command but it doesn't work in replacing spaces with tabs: awk=$'\'{OFS="\\t"}{print $1"\t"int(($3-$2)/2)+$2"\t"int(($3-$2)/2)+$2+1}\'' [me@me]$ echo $awk '{ ...
written 3.1 years ago by mujupas40
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Comment: A: Replace BED intervals
... Ok, thanks a lot, I'll give it a try! ...
written 3.1 years ago by mujupas40
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Replace BED intervals
... Hi! I want to make all the intervals in a series of BED files equal to 1bp by taking the middle position of each interval. Any suggestion about how to do it (possibly also with GNU Parallel?) Example: chr1 150 170 + I'd like to replace it as: chr1 160 161 + Thank you in advan ...
bed script written 3.1 years ago by mujupas40 • updated 3.1 years ago by ole.tange2.8k
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Answer: A: Statistical analysis on tags mapping in binned chromosomes intervals
... Ok, I will try them, thanks a lot! ...
written 3.1 years ago by mujupas40

Latest awards to mujupas

Popular Question 3.1 years ago, created a question with more than 1,000 views. For Extract rows from BED file on the base of text content in one column
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Graph of BED data on Chromosomes

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