User: Korsocius

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Korsocius160
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Posts by Korsocius

<prev • 49 results • page 1 of 5 • next >
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Comment: A: Error in SAM to BAM conversion
... Or sometimes check md5sum, if fastq files are downloaded correctly.. ...
written 13 months ago by Korsocius160
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Comment: C: How to combine multiple tools to detct SVs in WES data
... From my experience the best combination is pindel +CNVkit+ONCOcnv ;-) ...
written 2.3 years ago by Korsocius160
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Comment: C: Parallel for bwa mem - problem with -R argument for ID and SM
... Make file looks like the best option for all these process :-), i tried it without quotes, but I received error log : No input for ID..... ...
written 2.3 years ago by Korsocius160
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Comment: C: Using parallel with Mem
... https://www.biostars.org/p/302699/ ...
written 2.3 years ago by Korsocius160
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Parallel for bwa mem - problem with -R argument for ID and SM
... Dear all, I need help with the Read group ID and SM. I have parallel syntax to alignment via bwa mem. ls *R1_001.fastq | parallel 'bwa mem -k 19 -A 1 -B 4 -O 6 -L 5 -R '@RG\tID:'{.}'\tSM:'{.}'\tLB:'Trusight_custom_amplicon_CARR'\tPL:'ILLUMINA'\tPI:150' $REFERENCE {} {= s/_R1_001/_R2_001/ =} & ...
parallel alignment bwa written 2.3 years ago by Korsocius160 • updated 16 months ago by ATpoint36k
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Answer: A: Using parallel with Mem
... There is snytax for parallel with bwa mem, but I can't load ID and SM from INPUT. Do you know, where could be a problem? ls *R1_001.fastq | parallel 'bwa mem -k 19 -A 1 -B 4 -O 6 -L 5 -R '@RG\tID:'{.}'\tSM:'{.}'\tLB:'Trusight_custom_amplicon_CARR'\tPL:'ILLUMINA'\tPI:150' $REFERENCE {} {= s/_R ...
written 2.3 years ago by Korsocius160
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Comment: C: Awk command for fastq read length and number of reads?
... gunzip -c SRR1060507_1.fastq.gz | awk 'NR%4==2{print length($0)}' -for length gunzip -c SRR1060507_1.fastq.gz | awk 'END {print NR/4}' -for num. of sequences ...
written 2.4 years ago by Korsocius160
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Answer: A: Software To Call Somatic Indels?
... Really good and robust tool is CNVkit. py, but it is separate from somatic calling. I am using a samtools.. | varscan somatic and in other branch CNVkit, ther are some limitations, but it is work well. ...
written 2.4 years ago by Korsocius160
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Comment: C: Is it possible to run variant calling software in parallel, are there any Shell
... Peirre , can I have another question, please? Is it possible to run two makefiles in once time, because varscan calls separately snps and indels. If I tried to add another row to makefile with "samtools...... | varscan mpileup2snp..." second command was not parallelized. I tired this, but doesn't ...
written 2.4 years ago by Korsocius160
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Comment: C: Is it possible to run variant calling software in parallel, are there any Shell
... It works, thank you. ...
written 2.4 years ago by Korsocius160

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Popular Question 5 months ago, created a question with more than 1,000 views. For bedtools probelm of syntax
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Popular Question 22 months ago, created a question with more than 1,000 views. For bedtools probelm of syntax
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