User: Rob

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Rob70
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Posts by Rob

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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 5 days ago by Rob70
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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 7 days ago by Rob70 • updated 7 days ago by Alex10
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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 5 weeks ago by Rob70
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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 5 weeks ago by Rob70
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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 5 weeks ago by Rob70
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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 5 weeks ago by Rob70
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Comment: C: Samtools: merge and mpileup vs mpileup alone for variant-calling with multiple B
... But what mpileup do with the 2 files informations? Since it's the same sample (with identical @RG tag), does not it merge them together too? ...
written 5 weeks ago by Rob70
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Comment: C: how to parse blast output using biopython
... I think you are 2 years late.. And everything about biopython is writen [here][1] [1]: http://biopython.org/DIST/docs/tutorial/Tutorial.html ...
written 5 weeks ago by Rob70
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Comment: C: how to parse blast output using biopython
... Biopython doesn't totally support the plain text parsing now, not enough stable, so XML is the best recommanded output for Biopython parsing. ...
written 5 weeks ago by Rob70
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Samtools: merge and mpileup vs mpileup alone for variant-calling with multiple BAM
... Hi, I'm doing some variant-calling, and I was wondering what is the difference between: merging BAM files with samtools merge and call samtools mpileup on the merged BAM and skip the merge step and call mpileup with all the BAM files? I did both and expected the same results, but I got 15% of id ...
variant-calling merge samtools mpileup snp written 5 weeks ago by Rob70

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Popular Question 5 months ago, created a question with more than 1,000 views. For How to properly merge multiple runs into one bam file ?
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