User: by0

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by0110
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Posts by by0

<prev • 13 results • page 1 of 2 • next >
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Answer: A: How To Generate A Bibtex File From Pmids
... http://pubtex.herokuapp.com/ ...
written 24 months ago by by0110
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Comment: C: Dbsnp : Best Way To Obtain Data On Snps
... try change to snp.db <- useMart("ENSEMBL_MART_SNP", dataset="hsapiens_snp") and filters="snp_filter" ...
written 3.1 years ago by by0110 • updated 13 months ago by RamRS24k
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Comment: C: Ideal samtools view f/F flags
... Ah forgot to mention. I'm using the bam for SNP calling using freebayes ...
written 4.4 years ago by by0110
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Ideal samtools view f/F flags
... I'm filtering my sam file using the following command: samtools view -Sb -f 2 -F 256 after doing some research I think I've figured out what the flags mean (correct me if I'm wrong). -f 2 is keeping only reads that are "properly aligned according to the aligner" -F 256 is discarding "secondary ...
wgs next-gen samtools alignment sequencing written 4.4 years ago by by0110 • updated 4.4 years ago by alolex900
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Comment: C: Benchmarking TFBS in yeast
... None that are annotated and readily accessible from a database in the public domain for yeast. Thanks for the tip though. ...
written 4.6 years ago by by0110
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Comment: C: Benchmarking TFBS in yeast
... Let me clarify, I meant functional tfbs. My filtering is in effort to identify functional tfbs. I will update the question ...
written 4.6 years ago by by0110
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Benchmarking TFBS in yeast
... Hi, I am constructing my own position weight matrices (PWMs) and scoring regions of the yeast genome, for a list of predicted TFBS. I am then using different features to filter this list, in effort to minimize the false positive rate.  My question is, since there is no experimentally defined funct ...
tfbs expression pwm benchmark transcription written 4.6 years ago by by0110
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Answer: A: How To Define A Protein As Kinase Protein?
... You shouldn't use GO terms to define protein kinases. There are more sophisticated ways to make these predictions, such as sequence scanning, on a domain level. A solution would be to use HMMER, combined with the kinomer library (this is similar to what PFAM does), except it will predict on a kinase ...
written 5.2 years ago by by0110
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Motif enrichment using motif-x: how to pick significant motifs
... Hello,   I'm carrying out motif enrichment on a set of 15-mer kinase substrate peptides using motif-x, which results in something like this (see below). Now, I'm trying to select the most significant motifs. According to motif-x, all returned motifs are significantly enriched, but In this case th ...
significant enrichment motif-x motif peptide written 5.2 years ago by by0110
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Answer: A: Creating Sequence Logos From The Command Line
... Check out RWebLogo. It's an R wrapper for the WebLogo python library. It can be downloaded from CRAN: http://cran.r-project.org/web/packages/RWebLogo/index.html and is hosted on github: https://github.com/omarwagih/RWebLogo           ...
written 5.5 years ago by by0110

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Popular Question 24 months ago, created a question with more than 1,000 views. For Ideal samtools view f/F flags
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Ideal samtools view f/F flags
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Precomputed secondary structure prediction from sequence
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Precomputed secondary structure prediction from sequence

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