User: Paul

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Paul820
Reputation:
820
Status:
Trusted
Location:
European Union
Last seen:
11 hours ago
Joined:
3 years, 9 months ago
Email:
b********@gmail.com

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Posts by Paul

<prev • 120 results • page 1 of 12 • next >
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Answer: A: How To Sort Bed Format File
... I am using simply: sort -k 1V,1 -k 2n,2 input.bed ...
written 5 days ago by Paul820
5
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1
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93
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1
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Answer: A: KEGG data parse
... Hi, this solution works on your example data. I just erase first column and substitute `spaces` with `comma`. Then used `translate` and `paste` command. Finally add header to your requirements. This works in case we still have the same number of rows. Please test it. awk -v OFS="," '$1=$1' IN ...
written 5 days ago by Paul820
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Comment: C: cvnkit: what is the problem here?
... Hi, what version python do you have - `python --version` ? And did you install cnvkit from anaconda, pip or git? ...
written 23 days ago by Paul820
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Answer: C: Is bcf just a bgzipped vcf?
... BCF is binary counterpart of VCF file. Please look [here][1] for description. Similar to SAM vs BAM. [1]: https://samtools.github.io/bcftools/bcftools.html ...
written 28 days ago by Paul820
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Comment: C: bedtools intersect bed and vcf, coordinates problem
... Hi, Could you tried please modify your bed file: 1 100 100 and then use syntax - bedtools intersect -a in1 -b in2 -wao ...
written 4 weeks ago by Paul820
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Comment: C: Mask or trim primer sequences in Amplicon sequencing
... Thank you for good article. ...
written 6 weeks ago by Paul820
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3
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225
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Comment: C: filter DNA sequences of defined length for certain bases at exact positions
... Please if you can mark answer or up-vote any solution above. ...
written 11 weeks ago by Paul820
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Comment: C: filter DNA sequences of defined length for certain bases at exact positions
... What is an input file? FASTA? ...
written 11 weeks ago by Paul820
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Comment: A: fasta files: keep only lines containing certain characters + the respective sequ
... Hi, if you want to use grep, just try: grep -w "18S" -A 1 input.fasta > 18S.fasta parameter `A` means, that grep print one lines of trailing context. Parameter `w` match only whole word -in our case 18S. EDIT: This works only if you have in header 18S and no-where else. Also you need corre ...
written 12 weeks ago by Paul820
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Comment: C: Downloading genomic interval for hg38
... Hi, please look at [UCSC][1] genome browser and select table - you can get print all required informations. [1]: https://genome.ucsc.edu/cgi-bin/hgTables ...
written 3 months ago by Paul820

Latest awards to Paul

Appreciated 2 days ago, created a post with more than 5 votes. For A: How To Filter Mapped Reads With Samtools
Good Answer 5 days ago, created an answer that was upvoted at least 5 times. For C: Is bcf just a bgzipped vcf?
Good Answer 5 days ago, created an answer that was upvoted at least 5 times. For A: Compare two matrix
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: Fastq Convert To Fasta
Appreciated 28 days ago, created a post with more than 5 votes. For A: How To Filter Mapped Reads With Samtools
Scholar 28 days ago, created an answer that has been accepted. For A: Help With Genotyping In My Vcf File
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: Fastq Convert To Fasta
Good Question 6 weeks ago, asked a question that was upvoted at least 5 times. For Mask or trim primer sequences in Amplicon sequencing
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Filter out specific reads from FASTQ files
Student 10 weeks ago, asked a question with at least 3 up-votes. For Calculating GC content from BAM file by BED file
Popular Question 11 weeks ago, created a question with more than 1,000 views. For How to extract contigs from FASTA file which contains specific sequence
Popular Question 3 months ago, created a question with more than 1,000 views. For How to compare assembly from Trinity and Velvet/Oases
Appreciated 4 months ago, created a post with more than 5 votes. For A: How To Filter Mapped Reads With Samtools
Scholar 4 months ago, created an answer that has been accepted. For A: Help With Genotyping In My Vcf File
Student 4 months ago, asked a question with at least 3 up-votes. For How to compare assembly from Trinity and Velvet/Oases
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Fastq Convert To Fasta
Popular Question 4 months ago, created a question with more than 1,000 views. For How to extract contigs from FASTA file which contains specific sequence
Appreciated 4 months ago, created a post with more than 5 votes. For bash loop for alignment RNA-seq data
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How To Filter Mapped Reads With Samtools
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How To Filter Mapped Reads With Samtools
Great Question 7 months ago, created a question with more than 5,000 views. For shell script for bowtie/bwa alignment pair end reads
Popular Question 7 months ago, created a question with more than 1,000 views. For After run Cufflinks - cuffdiff there is no information about isoforms, TSS, CDS...
Centurion 8 months ago, created 100 posts.
Appreciated 8 months ago, created a post with more than 5 votes. For Mask or trim primer sequences in Amplicon sequencing
Great Question 8 months ago, created a question with more than 5,000 views. For bash loop for alignment RNA-seq data

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