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Moderator: bioExplorer

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bioExplorer ♦ 3.7k
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Posts by bioExplorer

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Comment: C: How to install samtools v.1.2 on Ubuntu 14.0 32 bit?
... Coming back to my question after ~3 years with this answer **1. Install `conda`** Go to [this][1] link and download the appropriate miniconda installler. The file should look something like this `Miniconda2-latest-Linux-xxx_xx.sh` **2. Follow installation steps** Follow the steps mentioned at [t ...
written 3 days ago by bioExplorer ♦ 3.7k
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Comment: C: Splitting string in a column using character
... try this grep -P 'rs\d+' test.txt -o ...
written 4 days ago by bioExplorer ♦ 3.7k
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Comment: C: Splitting string in a column using character
... Can you paste an example how should your result look like? ...
written 4 days ago by bioExplorer ♦ 3.7k
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Answer: A: Splitting string in a column using character
... grep -P 'rs\d+\.?\d+?' test.txt -o where `test.txt` is the file containing the ids you have mentioned above **output** rs10136766 rs104894363 rs10774624 rs111647200 rs117306900 rs117306950 rs117306954 rs117306975 rs117306989 rs532891158.1 rs7947285 ...
written 4 days ago by bioExplorer ♦ 3.7k
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Comment: C: How to report genomic intervals essentailly overlapping in all files?
... It was a toy example from bedtools page as I had mentioned. Thanks https://www.biostars.org/u/36456/ for a quick response. I highly appreciate that :D ...
written 7 days ago by bioExplorer ♦ 3.7k
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Comment: C: How to report genomic intervals essentailly overlapping in all files?
... Seems like you forgot to make the change from bioinfo$ awk -v OFS='\t' -v files=files '$4==files' out to bioinfo$ awk -v OFS='\t' -v files=$files '$4==files' out correct ? ...
written 9 days ago by bioExplorer ♦ 3.7k
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Comment: C: How to report genomic intervals essentailly overlapping in all files?
... Works! But how can I modify such that `3` is replaced by the "count of file" ? This is because I want to automate that !! Thanks ...
written 9 days ago by bioExplorer ♦ 3.7k
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Comment: C: How to report genomic intervals essentailly overlapping in all files?
... This works but I cannot keep on writing names of all bed files one by one when I have 100's of files! ...
written 9 days ago by bioExplorer ♦ 3.7k
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Comment: C: How to report genomic intervals essentailly overlapping in all files?
... Hi https://www.biostars.org/u/40003/ I tried this so far, bioinfo$ for i in *.bed ; do echo $i ; echo ; cat $i ; echo ; done test1.bed chr1 20 30 test2.bed chr1 15 25 test.bed chr1 10 30 -- bioinfo$ bedtools multiinter -i test1.bed tes ...
written 9 days ago by bioExplorer ♦ 3.7k
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How to report genomic intervals essentailly overlapping in all files?
... Consider the following example from [bedtools intersect help page][1]. Say, there are 4 bed files as follows $ cat query.bed chr1 1 20 chr1 40 45 chr1 70 90 chr1 105 120 chr2 1 20 chr2 40 45 chr2 70 90 chr2 105 120 chr3 1 20 chr3 40 ...
bedtools bed bam written 10 days ago by bioExplorer ♦ 3.7k

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Popular Question 19 days ago, created a question with more than 1,000 views. For What are some good resources to learn shell script for NGS pipeline development?
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Popular Question 5 weeks ago, created a question with more than 1,000 views. For Where can I do an online project to get some hands on experience with NGS data analysis?
Appreciated 6 weeks ago, created a post with more than 5 votes. For C: bioinformatics phd .in distance education forum ...
Popular Question 8 weeks ago, created a question with more than 1,000 views. For What are some good resources to learn shell script for NGS pipeline development?
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Scholar 3 months ago, created an answer that has been accepted. For A: Just complement or reverse sequence fom Biopython, but not reverse-complement on
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Draw circular genome with selected features
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Draw circular genome with selected features
Scholar 4 months ago, created an answer that has been accepted. For A: Just complement or reverse sequence fom Biopython, but not reverse-complement on
Scholar 4 months ago, created an answer that has been accepted. For A: Just complement or reverse sequence fom Biopython, but not reverse-complement on
Popular Question 4 months ago, created a question with more than 1,000 views. For What are some good resources to learn shell script for NGS pipeline development?
Popular Question 4 months ago, created a question with more than 1,000 views. For What are some good resources to learn shell script for NGS pipeline development?
Popular Question 4 months ago, created a question with more than 1,000 views. For What are some good resources to learn shell script for NGS pipeline development?
Popular Question 4 months ago, created a question with more than 1,000 views. For How to install samtools v.1.2 on Ubuntu 14.0 32 bit?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Draw circular genome with selected features
Popular Question 4 months ago, created a question with more than 1,000 views. For How to install samtools v.1.2 on Ubuntu 14.0 32 bit?
Popular Question 5 months ago, created a question with more than 1,000 views. For Error encountered while running stattest from ballgown package
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Popular Question 7 months ago, created a question with more than 1,000 views. For Error encountered while running stattest from ballgown package
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