User: Rob

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Rob70
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Posts by Rob

<prev • 32 results • page 1 of 4 • next >
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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 days 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 3 days 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 3 days 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 3 days 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 3 days 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 3 days 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 3 days 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 3 days ago by Rob70
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Comment: C: Wrong version of data file with Fgenesh gene finder
... Hi, thanks for your concern. I was confused by the error message, but @h.mon was right, I didn't use a correct fgenesh database. Now it's good, except that it didn't currently work with my multifasta file, but only with the contigs one by one. Do you know if this is a normal behaviour? I got `Error ...
written 7 days ago by Rob70
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Comment: C: perl or the other scripts converting text file
... This is what people with homework assignment would say! ...
written 14 days ago by Rob70

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Popular Question 3 months ago, created a question with more than 1,000 views. For How to properly merge multiple runs into one bam file ?
Supporter 6 months ago, voted at least 25 times.

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