User: Ric
Ric • 190
- Reputation:
- 190
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- Location:
- Australia
- Last seen:
- 1 day, 12 hours ago
- Joined:
- 7 years, 1 month ago
- Email:
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Posts by Ric
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2
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... 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
Ric • 190
0
votes
0
answers
140
views
0
answers
... 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 ...
written 7 weeks ago by
Ric • 190
0
votes
1
answer
234
views
1
answer
... 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 ...
written 8 weeks ago by
Ric • 190
• updated
8 weeks ago by
Pierre Lindenbaum ♦ 116k
0
votes
1
answer
183
views
1
answers
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
Ric • 190
0
votes
1
answer
183
views
1
answers
Comment:
C: converting fast5 to fasta failed
... I tried all and 2d none of them have created an output. ...
written 11 weeks ago by
Ric • 190
1
vote
1
answer
183
views
1
answer
... 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, ...
written 11 weeks ago by
Ric • 190
• updated
11 weeks ago by
Heather Ward • 50
0
votes
1
answer
193
views
1
answers
... Thank you, is there a script for it? ...
written 11 weeks ago by
Ric • 190
0
votes
1
answer
193
views
1
answer
... 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 ...
written 11 weeks ago by
Ric • 190
1
vote
1
answer
267
views
1
answer
... 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 ...
0
votes
0
answers
202
views
0
answers
Comment:
C: bowtie2 unique align reads
... Thank you it worked. ...
written 12 weeks ago by
Ric • 190
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