User: mujupas

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mujupas50
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50
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Location:
Japan
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4 hours ago
Joined:
4 years, 8 months ago
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Posts by mujupas

<prev • 20 results • page 1 of 2 • next >
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Answer: A: Bowtie alignment of piRNAs to find potential targets
... Thank you, I'll try both options! ...
written 5 days ago by mujupas50
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Bowtie alignment of piRNAs to find potential targets
... Hi, I have a set of piRNAs in fasta format and I want to find their potential targets. According to literature nucleotides in position 1-10 in the piRNAs sequences should constitute the seed and do not tolerate any mismatch while nt 11-20 tolerate up to 3 mismatches. Bowtie can specify the length of ...
alignment pirna bowtie written 6 days ago by mujupas50
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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 months ago by mujupas50
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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 months ago by mujupas50
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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 16 months ago by mujupas50
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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 17 months ago by mujupas50
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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 17 months ago by mujupas50 • updated 17 months ago by Alex Reynolds24k
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Comment: C: Replace BED intervals
... Worked like a charm, thank you so much! ...
written 3.6 years ago by mujupas50
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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 3.6 years ago by mujupas50
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Comment: A: Replace BED intervals
... Ok, thanks a lot, I'll give it a try! ...
written 3.6 years ago by mujupas50

Latest awards to mujupas

Popular Question 9 months ago, created a question with more than 1,000 views. For Replace BED intervals
Popular Question 3.6 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 3.6 years ago, created a question with more than 1,000 views. For Graph of BED data on Chromosomes

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