User: Raymond301

gravatar for Raymond301
Raymond301160
Reputation:
160
Status:
New User
Location:
Rochester, MN
Website:
http://raymondmoore.wo...
Last seen:
6 years, 8 months ago
Joined:
9 years, 1 month ago
Email:
r***************@gmail.com

Occupation: Informatics Specialist FIRST Robotics Mentor

Posts by Raymond301

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Convert A Psl File To A Sam File And Also Write Sequences To The Sam File?
... This isn't that useful....examples should be included. ...
written 6.8 years ago by Raymond301160
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Obtain Genomic Position From Codon # & Refseq
... I have a large list of mutations, their codon # and I can map through the gene to a RefSeq Id (include the transcript version). I'd like to find the genomic position from this information, I would think that there is some API or tool, I'm still picking through Bio:Perl to see if there is anything ...
refseq written 8.5 years ago by Raymond301160 • updated 5.0 years ago by Reece270
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Comment: C: Problem Running Pindel With Bam Files
... Ah, that would do it. I'm sorry I couldn't be more help. ...
written 8.5 years ago by Raymond301160
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Answer: A: Problem Running Pindel With Bam Files
... I've used Novo Align successfully. There is one thing to note....Pindel will not work on Single End reads! Ensure that you're alignment contains paired reads. java -jar picard/1.55/CollectInsertSizeMetrics.jar I=<sorted.bam> H=<output histogram.png> O=<output stats.txt> samtool ...
written 8.5 years ago by Raymond301160
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Comment: C: Can Bcftools And Vaast Call Phased Genotypes?
... I'm also interested in this question! ...
written 8.5 years ago by Raymond301160
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Comment: C: Unable To Debug Pacbio Resource (Gfftovcf.Py) Module Error
... If you have a real gff to begin with then, http://www.smrtcommunity.com/SMRT-Analysis/Tools. The SMRT package is great. But I have a non-standard gff. ...
written 8.6 years ago by Raymond301160 • updated 12 months ago by RamRS30k
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How To Convert Breakpointer .Gff To .Vcf (Need To Understand Format)?
... I'm using Breakpointer, provided from https://github.com/ruping/Breakpointer However the output claims to be .gff. I've already tried to use the gffToVcf.py module provided by PacBio, however this .gff does not adhere to the same standards expected by PacBio. Here is an example of the format. chr ...
vcf gff format written 8.6 years ago by Raymond301160 • updated 8.6 years ago by Lars Juhl Jensen11k
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Comment: C: Unable To Debug Pacbio Resource (Gfftovcf.Py) Module Error
... Yes, you are correct! Python 2.5.1 causes FAILURE. Thank you so very much! ...
written 8.6 years ago by Raymond301160
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Answer: A: Mapping Snp Ids To Gene Symbol
... PharmGKB has a resource. However it is not a comprehensive list. http://www.pharmgkb.org/resources/downloads_and_web_services.jsp Download rsid.zip. ...
written 8.6 years ago by Raymond301160
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Comment: C: Best Free Text Editor For All Popular Languages (R, Python, Perl Etc..)
... +1 My Favorite. But plugins are a must have! ...
written 8.6 years ago by Raymond301160

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