User: ricardoguerreiro2121
ricardoguerreiro2121 • 20
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Posts by ricardoguerreiro2121
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... Thank you for the suggestion. I already had the answer I was looking for. The client wants an R script to run in windows, hehe. ...
written 9 weeks ago by
ricardoguerreiro2121 • 20
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... Perfect answer, thank you!
I didn't realize VCF[-c(1, 5, 7)] would subset the vcf like if it was a vector. It only prints the metainformation but when doing info(filteredVcf) you can can see that the rows are gone.
Once again thanks and have a nice day/evening! ...
written 9 weeks ago by
ricardoguerreiro2121 • 20
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... I know, right?? I initially did a python script and it was much easier, besides having better performance. But I need to deliver an R filter to a client that does not know (or even have installed) python... ...
written 9 weeks ago by
ricardoguerreiro2121 • 20
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... I have a filtering function that outputs desired indexes (based on, for example, the value of info(VCF)$MQ ) but I can't subscript VCF with indexes because it's not a dataframe or a vector. That is why I thought of parsing the raw lines as elements of a vector. I can just concatenate them to the hea ...
written 9 weeks ago by
ricardoguerreiro2121 • 20
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... Hello
Simple question ( I hope!)
I'm using this [VariantAnnotation][1] package from bioconductor to work with SNPs.
myparam = ScanVcfParam( # this function is a fast positional filter
samples="3441_pseudo_gatk",
which= GRanges(chr[14], # This is a chro ...
written 9 weeks ago by
ricardoguerreiro2121 • 20
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... Great, that's it, thanks! It depends on what is the query and what is the reference. Thanks! (If you write it as an answer instead of a comment I'll accept it) ...
written 10 weeks ago by
ricardoguerreiro2121 • 20
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... Hello,
A simple question. What is the sequence identity between 2 sequences when one is much larger than the other?
Example:
seq1: -------------------AGTGTGAAAAAGGT----------------
seq2: ATATATGCGCATGGTAATAAGTGTGAAAAAGGTTATATGCGCATAAGGT
The smaller sequence corresponds 100% to a subse ...
written 10 weeks ago by
ricardoguerreiro2121 • 20
• updated
10 weeks ago by
Bastien Hervé ♦ 4.0k
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... Brilliant! Sometimes you just have to go around the problems, not force your way through.
Danke schön!
Ricardo ...
written 3 months ago by
ricardoguerreiro2121 • 20
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... Hello,
I'm using the Pysam module of Python and calling the function:
VF = VariantFile("input_file")
VF.fetch()
seems to retrieve all reads in the file,
while this retrieves reads from positions 0 to 1000 in one specific contig:
VF.fetch(contig="contig_name", start=0, end=100 ...
written 3 months ago by
ricardoguerreiro2121 • 20
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Comment:
C: Capping coverage in bam file
... Once again simple, merci bien!
Keep up the helpfulness, it really makes a difference for starting researchers like me. ...
written 5 months ago by
ricardoguerreiro2121 • 20
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