User: Felix Francis

gravatar for Felix Francis
Felix Francis340
Reputation:
340
Status:
Trusted
Location:
United States/University of Delaware
Website:
https://sites.google.c...
Twitter:
ffrancis12
Last seen:
1 month, 2 weeks ago
Joined:
2 years, 6 months ago
Email:
f************@gmail.com

Bioinformatics, Systems Biology, Python, R, MySQL

Posts by Felix Francis

<prev • 25 results • page 1 of 3 • next >
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Answer: A: aligner for CORRECTED pacbio long reads
... I would use bwa mem or BLASTn rather than blasr for better specificity. I have had experience with mapping error corrected PacBio reads using blasr and some of the best hits were incorrect. ...
written 6 weeks ago by Felix Francis340
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Answer: A: convert json to gff
... You could use the following json2gff python script: http://pythonhosted.org/mgkit/scripts/json2gff.html usage: json2gff mongodb [-h] [-v | --quiet] [--cite] [--manual] [--version] [input_file] [output_file] ...
written 6 weeks ago by Felix Francis340
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Answer: A: Is it possible to create a restriction map using python?
... Check this out: http://biopython.org/DIST/docs/cookbook/Restriction.html https://www.youtube.com/watch?v=Q94PXqi8e8I ...
written 11 months ago by Felix Francis340
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Answer: A: gene and disease nework
... If you have a list of proteins/genes and their aggregate p-values from a GWAS study or transcriptome analysis study, you could use HotNet2(https://github.com/raphael-group/hotnet2) to prioritize significantly mutated subnetworks. Also, see FunSeq2(http://funseq2.gersteinlab.org/) ...
written 11 months ago by Felix Francis340
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Answer: A: SNP calling with fasta files
... If you are dealing with two assembled genomes, you could use a genome aligner such as MAUVE http://gel.ahabs.wisc.edu/mauve/ to identify the divergent regions(including SNPs) between them. You can write a simple script to convert this data to VCF format.   ...
written 22 months ago by Felix Francis340
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Answer: A: List record in a local BLAST database
... Use "fastacmd" to generate a single fasta file from an existing BLAST database You can use the following arguments along with it: -d    BLAST database (the default is "nr") -D    1 (dump the database in fasta format) -o    filename for the output Example: fastacmd -d cdna -D 1 -o seq.fasta   ...
written 22 months ago by Felix Francis340
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Comment: C: How to count the number of shared (the same) nucleotides between any two sequenc
... Alignment tools like mafft, muscle etc. does this for you if you are not comfortable with writing a script to compare all possible k-mers/aligned bases between all pairwise sequences to construct a distance matrix. Follow the steps given in this link: http://mafft.cbrc.jp/alignment/software/treeout ...
written 23 months ago by Felix Francis340
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Answer: A: Please share the best tool for de novo motif discovery in large dataset
... Detection rate for any individual motif prediction tool alone is bad whether its is for small or large data sets. The best approach is to use a combination different tools to get more reliable results.  Some of the best ranked ones are: Meme, MotifSampler and Weeder (ref: Tompa et al., Assessing co ...
written 23 months ago by Felix Francis340
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Answer: A: How to count the number of shared (the same) nucleotides between any two sequenc
... Run this python code : https://github.com/ffrancis/bioinformatic_algorithms/blob/master/codes/1_11_HammingDistance_pattern_match.py You need to have the inputs p and q as each of the sequences in your algnment ...
written 23 months ago by Felix Francis340
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Ideal coverage required for PacBio error correction using HGAP
... What is the ideal PacBio coverage required for error correction (consensus polishing) using HGAP (by only using PacBio reads)? How effective is this approach in error correction? How does this approach compare with hybrid error correction using Illumina short reads (assuming the reads are from a ho ...
illumina hgap error correction pacbio written 23 months ago by Felix Francis340

Latest awards to Felix Francis

Appreciated 11 months ago, created a post with more than 5 votes. For A: NGS reads simulation
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: NGS reads simulation
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: NGS reads simulation
Good Answer 2.1 years ago, created an answer that was upvoted at least 5 times. For A: NGS reads simulation
Appreciated 2.1 years ago, created a post with more than 5 votes. For A: NGS reads simulation
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: NGS reads simulation

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