User: predeus

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predeus400
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http://bioinf.me/research
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APredeus
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Posts by predeus

<prev • 51 results • page 1 of 6 • next >
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Answer: A: What is the expected rate of SNPs within a human exome sequencing with HiSeq?
... The original number is insanely low, and Wouter's number is very, very high. A good place for reference is flagship ExAc paper: https://www.nature.com/articles/nature19057 Normal number of variants is approximately 1 per 1kb of exonic sequence. More precisely, about 25,000 variants for European, ...
written 15 days ago by predeus400
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Answer: A: How to segregate metagenomic sequences in prokaryotic and eukaryotic groups
... Ok, I know this is a really old thread, but anyways: you're getting a very low taxonomy assignment in Kraken since you are using the default database, which is composed of known bacteria and viruses. You need something with eukaryotes in it, probably nt database (the default setting for Web blastn). ...
written 16 days ago by predeus400
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Comment: C: Version history and design files for exome kits from Agilent, Roche(Nimblegen),
... Thank you, this is useful. The field is changing so rapidly. It's good to keep track of what's going on. ...
written 10 weeks ago by predeus400
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Version history and design files for exome kits from Agilent, Roche(Nimblegen), and Illumina
... Hello all, I am working on comparison of exome kits and came to understand that it can be quite hard to understand what's offered in the market and what are their relative advantages. So I made this topic dedicated to collecting of information about exome kits from the three major providers: Agile ...
exome agilent roche nimblegen illumina written 10 weeks ago by predeus400 • updated 10 weeks ago by tjduncan100
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Comment: C: Bed For Agilent Sureselect All Exon Kits ?
... They are certainly still there, starting with version 4.0 ...
written 10 weeks ago by predeus400
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Comment: C: How to change Bioperl's Bio::SeqIO default sequence folding?
... Ahh, was staring right at it. Thanks again. ...
written 4 months ago by predeus400
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Comment: C: How to change Bioperl's Bio::SeqIO default sequence folding?
... great, thanks. Where in the docs is it? Couldn't find it when I looked ...
written 4 months ago by predeus400
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How to change Bioperl's Bio::SeqIO default sequence folding?
... Hello all, I've been using Bioperl for some time, but not too much. A simple question came up and I'm not sure how to handle it. When using write_seq function, it folds the sequence at 60 characters by default. How can I change this number or stop folding completely? I can re-fold the sequence w ...
fasta fastq bioperl written 4 months ago by predeus400 • updated 4 months ago by Chris Fields1.8k
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Annotate multiple rRNAs with variable and constant regions
... Hello all, I was wondering what ways are there to annotate the multiple rRNA alignments with the relative position on 16S (or 18S) consensus. To put it simply, I'd like to know for each sequence where are the approximate V1 borders, and so on. I would appreciate hearing any ideas. ...
multiple alignment rrna silva written 6 months ago by predeus400
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Answer: A: Have anybody converted exome bam files to .tdf files for visualization in IGV?
... Basically -e adds extra coverage to your reads, which is annoying and can be misleading. If the sequencing is paired-end, you'll see both reads, so there's no real reason to extend the coverage past what's actually seen in the reads. I would say just set it to 0 for all applications. Go ahead and ...
written 7 months ago by predeus400

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Prophet 15 days ago, created a post with more than 20 followers. For Duplicates on Illumina
Popular Question 7 months ago, created a question with more than 1,000 views. For Chip-Seq Of Conventional Tfs: What Are The Peaks W/O The Motif?
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: How To Convert Gencode Gtf Into Bed Format ?
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Popular Question 12 months ago, created a question with more than 1,000 views. For How To Determine If Library Is Strand-Specific
Appreciated 12 months ago, created a post with more than 5 votes. For Duplicates on Illumina
Good Question 12 months ago, asked a question that was upvoted at least 5 times. For Duplicates on Illumina
Student 12 months ago, asked a question with at least 3 up-votes. For Duplicates on Illumina
Popular Question 20 months ago, created a question with more than 1,000 views. For Chip-Seq Of Conventional Tfs: What Are The Peaks W/O The Motif?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Find All Annotated Rrna (Rdna) Sequences
Popular Question 3.3 years ago, created a question with more than 1,000 views. For How To Determine If Library Is Strand-Specific
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Find All Annotated Rrna (Rdna) Sequences
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Too late to switch to Bioinformatics?

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