User: Paul

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Paul640
Reputation:
640
Status:
Trusted
Location:
European Union
Last seen:
1 day, 19 hours ago
Joined:
3 years, 7 months ago
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b********@gmail.com

about me

Posts by Paul

<prev • 114 results • page 1 of 12 • next >
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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 26 days ago by Paul640
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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 26 days ago by Paul640
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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 4 weeks ago by Paul640
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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 7 weeks ago by Paul640
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Comment: C: SNP data filtering from VCF file
... Hi, no Varscan is variant caller - it generates VCF from BAM file (mpileup). Did you tried [this][1] Pierre solution? [1]: https://www.biostars.org/p/7403/ ...
written 10 weeks ago by Paul640
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Comment: C: Compare two matrix
... Your are welcome. Sorry for bash solution - I am not familiar with perl. ...
written 10 weeks ago by Paul640
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Answer: A: Compare two matrix
... Hi, what about this bash solution: > paste -d '\n' matrix1 matrix2 | awk 'NR>1' | grep -v "\bP1\b" | awk '{if(! a[$1]){print; a[$1]++}}' CDS BC1-III BC1-IV BC10-II LOC105031928 175 181.5 99 LOC105031930 NA NA ...
written 10 weeks ago by Paul640
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Comment: C: SNP data filtering from VCF file
... Hi, what variant caller do you use? Some of them have an option to call INDELS and SNP separately - for example VarScan.. ...
written 10 weeks ago by Paul640
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Comment: C: Mask or trim primer sequences in Amplicon sequencing
... So you prefer to hard trim FASTQ files from primer sequences instead of soft clipping in BAM? ...
written 3 months ago by Paul640
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Answer: A: Best Copy Number Variation Tools
... Hi, I have very good experiences with CNVkit - this is very robust tool and works perfectly fine for Capture enrichment library (also author mention good results for WGS and Amplicon panels, but did not validate). We are right now validating this tool and looks perfectly fine. This tool is very fast ...
written 3 months ago by Paul640

Latest awards to Paul

Student 14 days ago, asked a question with at least 3 up-votes. For Calculating GC content from BAM file by BED file
Popular Question 25 days ago, created a question with more than 1,000 views. For How to extract contigs from FASTA file which contains specific sequence
Popular Question 8 weeks ago, created a question with more than 1,000 views. For How to compare assembly from Trinity and Velvet/Oases
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: How To Filter Mapped Reads With Samtools
Scholar 9 weeks ago, created an answer that has been accepted. For A: Help With Genotyping In My Vcf File
Student 9 weeks ago, asked a question with at least 3 up-votes. For How to compare assembly from Trinity and Velvet/Oases
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Fastq Convert To Fasta
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
Appreciated 3 months ago, created a post with more than 5 votes. For bash loop for alignment RNA-seq data
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How To Filter Mapped Reads With Samtools
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How To Filter Mapped Reads With Samtools
Great Question 5 months ago, created a question with more than 5,000 views. For shell script for bowtie/bwa alignment pair end reads
Popular Question 6 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 6 months ago, created 100 posts.
Appreciated 6 months ago, created a post with more than 5 votes. For Mask or trim primer sequences in Amplicon sequencing
Great Question 6 months ago, created a question with more than 5,000 views. For bash loop for alignment RNA-seq data
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How To Filter Mapped Reads With Samtools
Appreciated 7 months ago, created a post with more than 5 votes. For Mask or trim primer sequences in Amplicon sequencing
Student 7 months ago, asked a question with at least 3 up-votes. For How to compare assembly from Trinity and Velvet/Oases
Popular Question 8 months ago, created a question with more than 1,000 views. For After run Cufflinks - cuffdiff there is no information about isoforms, TSS, CDS...
Popular Question 9 months ago, created a question with more than 1,000 views. For Using Bash For Gatk Pipeline
Student 10 months ago, asked a question with at least 3 up-votes. For How to compare assembly from Trinity and Velvet/Oases
Popular Question 11 months ago, created a question with more than 1,000 views. For Different coverage from bedtools and in vcf file - HELP PLEASE
Popular Question 11 months ago, created a question with more than 1,000 views. For Calculating GC content from BAM file by BED file
Popular Question 11 months ago, created a question with more than 1,000 views. For Filter out specific reads from FASTQ files

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