User: Ric

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Ric190
Reputation:
190
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Location:
Australia
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1 day, 12 hours ago
Joined:
7 years, 1 month ago
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m*******@gmail.com

Posts by Ric

<prev • 164 results • page 1 of 17 • next >
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Comment: C: bwa mem: Passing a variable to read group
... My header looks different: > zcat OZBenth2_R1.fq.gz | head -n 1 @HWI-ST945_0069:2:1101:1483:1976#GNNNNN/1 > echo $(echo $header | head -n 1 | cut -f 1-4 -d":" | sed 's/@//' | sed 's/:/_/g') HWI-ST945_0069_2_1101_1483 > echo $(echo $header | head -n 1 | grep -Eo "[ATGCN] ...
written 2 days ago by Ric190
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vcf to venn diagram
... Hi, I tried to reproduce this [article](https://justinbagley.rbind.io/2018/07/25/how-to-find-common-variants-in-multiple-vcf-files/) but this command failed: $ bcftools isec -n +2 calls-16c-gt-q20.vcf calls-SA-gt-q20.vcf > isec_file1-v-2_out.vcf [main] Unrecognized command. I am using ...
snp written 7 weeks ago by Ric190
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Failed to open var.raw.bcf: unknown file type
... Hi, I used the following commands to call SNPs samtools merge ${1}/all.sorted.dedup.bam ${1}/*.sorted.dedup.bam samtools index ${1}/all.sorted.dedup.bam samtools faidx $2 samtools mpileup -uf $2 ${1}/all.sorted.dedup.bam | bcftools view -bvcg - > var.raw.bcf bcftools v ...
snp written 8 weeks ago by Ric190 • updated 8 weeks ago by Pierre Lindenbaum116k
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Comment: C: converting fast5 to fasta failed
... We ask sequence company to sequence our genome. Is there any other software available? ...
written 11 weeks ago by Ric190
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Comment: C: converting fast5 to fasta failed
... I tried all and 2d none of them have created an output. ...
written 11 weeks ago by Ric190
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converting fast5 to fasta failed
... I tried to use poretoos to convert fast5 to fasta file but the below command did not create any file > poretools fasta --type best 15 > poretools fasta --type best 15/* > poretools fasta --type best 15/*.fast5 What did I miss you? Thank you in advance, ...
sequence written 11 weeks ago by Ric190 • updated 11 weeks ago by Heather Ward50
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Comment: C: Using flowcell name as file name for FASTQ file
... Thank you, is there a script for it? ...
written 11 weeks ago by Ric190
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Using flowcell name as file name for FASTQ file
... I have two folders and each of them contain the same file names. ls -1 10_S0_L001_R1_001.fastq.gz 10_S0_L001_R2_001.fastq.gz 11_S0_L001_R1_001.fastq.gz 11_S0_L001_R2_001.fastq.gz Is there a way to extract from each dataset the flowcell name and use it as unique filename? Thank ...
sequence next-gen written 11 weeks ago by Ric190
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samtools mpileup to bcftools mpileup
... I got samtools mpileup option `u` is functional, but deprecated. Please switch to using bcftools mpileup in future. How could I convert the following commands to bcftools mpileup ? samtools mpileup -uf QMg-NbQ3P-RN.fasta aln_P1O1.sorted.bam | bcftools view -bvcg - > P1O1_var.raw.bcf ...
bcftools samtools snp written 12 weeks ago by Ric190 • updated 12 weeks ago by zx87546.5k
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Comment: C: bowtie2 unique align reads
... Thank you it worked. ...
written 12 weeks ago by Ric190

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