User: Rob

gravatar for Rob
Rob120
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Joined:
4 years, 8 months ago
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Posts by Rob

<prev • 38 results • page 1 of 4 • next >
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Comment: C: how to de novo assemble a large number of bacterial genome with spades in Linux
... Type bash loop in google. ...
written 8 months ago by Rob120
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Answer: A: how to identify amino acids using snpEFF
... When the mutation is outside a coding region snpEff will not give you the potential amino acid change because there is no amino acid. If you look in coding region you will find amino acid modification: c.10G>A (It mean that in the 10th amino acid of this protein the G became an A) ...
written 14 months ago by Rob120
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Wrong genotype assignation in GATK?
... Hello, I am looking at some GATK VCF results, and I found something I can't explain. There is this result for one of my SNP: GT:AB:AD:DP:GQ:MQ0:PL 0/1:1.00:21,0:22:79:0:79,0,708 The concerned field is the AD which is the "*Allelic depths for the ref and alt alleles in the order listed*". ...
vcf gatk genotype snp written 2.4 years ago by Rob120
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Comment: C: Software for Tree Visualization
... No other software since 6.3 years? ...
written 3.3 years ago by Rob120
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Comment: C: De novo pacBio genome assembly: How to polish data without quiver?
... Well, I use Canu alone, and it don't contain a polisher. I wll try to use the pacBio polisher. ...
written 3.5 years ago by Rob120
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De novo pacBio genome assembly: How to polish data without quiver?
... I am currently working on some de novo genome assembly with pacBio data. I used Canu for assembly but I didn't have access to quiver (or arrow) for data polishing. What can I do now? I can't find any tools for replace quiver, so I'm a little bit stuck... Thanks ! ...
quiver sequencing polishing pacbio assembly written 3.5 years ago by Rob120 • updated 15 months ago by colindaven2.3k
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Comment: C: Samtools: merge and mpileup vs mpileup alone for variant-calling with multiple B
... Yep, only one sample (same RG tag for each Lane) ...
written 3.6 years ago by Rob120
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Comment: C: Samtools: merge and mpileup vs mpileup alone for variant-calling with multiple B
... The strange things with this is that I have more coverage on a single SNPs without merge the files before. Here one example (same for all SNPs common in both methods) : Ref Alt QUAL GT DP Without merge: T C 48.0158 0/1 26 With merge ...
written 3.6 years ago by Rob120
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Comment: C: Samtools: merge and mpileup vs mpileup alone for variant-calling with multiple B
... But since the RG tags are identical for one sample, doesn't mpileup merge files itself? And so the coverage should be identical compared to the step with merge no? ...
written 3.6 years ago by Rob120
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Comment: C: Samtools: merge and mpileup vs mpileup alone for variant-calling with multiple B
... I will try more research, because yeah, that is the information I'm looking for :) So which way do you personally suggest as the best? Merge first sample with same RG tags, and do variant calling on the merged file? ...
written 3.6 years ago by Rob120

Latest awards to Rob

Great Question 2.3 years ago, created a question with more than 5,000 views. For How to properly merge multiple runs into one bam file ?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For PacBio genome assembly with canu shorter than expected
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Samtools: merge and mpileup vs mpileup alone for variant-calling with multiple BAM
Popular Question 2.3 years ago, created a question with more than 1,000 views. For De novo pacBio genome assembly: How to polish data without quiver?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Samtools: merge and mpileup vs mpileup alone for variant-calling with multiple BAM
Voter 3.3 years ago, voted more than 100 times.
Popular Question 3.9 years ago, created a question with more than 1,000 views. For How to properly merge multiple runs into one bam file ?
Supporter 4.1 years ago, voted at least 25 times.

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