User: XIA.PAN

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XIA.PAN20
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Posts by XIA.PAN

<prev • 17 results • page 1 of 2 • next >
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Comment: C: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3
... It worked! Thank you ...
written 12 months ago by XIA.PAN20
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Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 30.
... Dear all, I need to filter a QualityScaledDNAStringSet that have less than 10% of the nucleotide having a Q score less than 30. I can get the numbers of Q scores in a list with as(quality(Set), "IntegerList") How can I apply the calculation? Thank you! ...
q score written 12 months ago by XIA.PAN20 • updated 12 months ago by Martin Morgan ♦♦ 23k
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Answer: A: Biostrings translate alt_init_codons, rule doesn't apply, how to get rid of the
...  attr(GENETIC_CODE, "alt_init_codons")=character(0)  works ...
written 14 months ago by XIA.PAN20
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Comment: C: Biostrings translate() function with alternative genetic code is not working for
... Dear Herve, I am translating a set of DNA sequences to peptides, therefore the alternative initiation codon doesn't apply. How can I reset the attribution? Thank you. Xiaoyan Hi, I tried  attr(GENETIC_CODE, "alt_init_codons")=NULL won't work, but  attr(GENETIC_CODE, "alt_init_codons")=character(0 ...
written 14 months ago by XIA.PAN20
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Biostrings translate alt_init_codons, rule doesn't apply, how to get rid of the attribution
... Hello, I need to translate a DNAstringSet to AAstringSet, where the alternative initiation codons doesn't apply.  How can I get rid of the attribution? Tried to set attr(GENETIC_CODE, "alt_init_codons")=NULL, but won't work. Thank you. Xiaoyan ...
biostrings translate written 14 months ago by XIA.PAN20
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Q score filter to each base in QualityScaledDNAStringSet
... Dear all, I have a QualityScaledDNAStingSet and want to filter out reads that have bases below a quality threshold (say 20 for instance).  I can get the Q score one by one using as.integer(DNA_seqs@quality[1]) Is there a function to get the Q score of each object in the QualityScaledDNAStringSet ...
qualitycontrol written 2.2 years ago by XIA.PAN20 • updated 2.2 years ago by Mike Smith3.5k
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Answer: A: how to deal with multiple barcodes/index in the analysis
... Hi James, I am trying to compare the DNA sequences and their frequencies in Table B1-B12. I would like to cbind all 12 tables to a data.frame and normalize each freq to the total seqs number.  But the number of DNA sequences and their frequencies in each Bi file are different. cbind ignores the NAs ...
written 2.2 years ago by XIA.PAN20
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how to deal with multiple barcodes/index in the analysis
... Dear all, I have a set of NGS data, that barcoded from B1 to B12, each one of the codes represents one sample. I need to apply analysis/calculation on these samples and I often find myself writing multiple lines, for example, convert multiple tables to multiple data.frames using the following: B1 ...
dnastringset aastringset written 2.2 years ago by XIA.PAN20
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Comment: C: How to get rid of the AAStrings with a stop codon
... The AAs in certain position are fixed, the rest are random, eg: L is located at the first, fourth and last position. So I use substr and paste to replace the random AAs to A and then apply vcountPattern/vmatchPattern. A big thank you!   ...
written 2.2 years ago by XIA.PAN20
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Comment: C: How to get rid of the AAStrings with a stop codon
... Thank you. Regarding the pattern filter, fixed=FALSE can only be used for DNASting and RNAString. when use vmatchpattern or vcountpattern with 'X' (extended IPUAC code), all return with no match. CompareStrings("LXXXLXXXL",seqs.frame$aa[1]) returns "L???L???L"---fit and "?????????" --non-fit.   But ...
written 2.2 years ago by XIA.PAN20

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Popular Question 12 months ago, created a question with more than 1,000 views. For translate DNA sequence to Amino acid sequence in a dataframe

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