User: neal.platt

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neal.platt220
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Posts by neal.platt

<prev • 21 results • page 1 of 3 • next >
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Answer: A: Mrbayes Produces Incorrect Tree When Run In Mpi Mode
... We have the same problem (large polytomies). Take your data and run the "sumt" command in MrBayes3.1 and you will recover the appropriate tree. ...
written 5.6 years ago by neal.platt220
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Comment: C: Question About Bwa Pe Mapping And Calling "Properly Mapping Pairs" In Samtools
... You are right I was using the wrong fastq file for the given .sai. I appreciate your help more than you know. ...
written 6.3 years ago by neal.platt220
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Comment: C: Question About Bwa Pe Mapping And Calling "Properly Mapping Pairs" In Samtools
... I have updated with information from the SAM file. Thanks. ...
written 6.3 years ago by neal.platt220
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Question About Bwa Pe Mapping And Calling "Properly Mapping Pairs" In Samtools
... I am using BWA to map PE reads from 300-400bp fragments to a reference genome. After mapping I am using SAMtools to filter out "properly mapping pairs" using the -f 0x002 option. Here is my BWA/SAMtools syntaxt $> bwa aln -t 12 -f <input index read 1> myoLuc2.bwa.bwtsw <read 1 fastq& ...
samtools bwa filtering written 6.3 years ago by neal.platt220 • updated 5.5 years ago by Biostar ♦♦ 20
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Answer: A: List Of Bioinformatics Books
... Practical Computing for Biologists This is the best intro book out (IMO) ...
written 6.5 years ago by neal.platt220
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Comment: C: Differences Between Ucsc And Local Repeatmasker Results
... Are you supplying the library using the '-lib' option or are you using the '-species' option. Do you mind sharing the annotation you are expecting versus what RM is giving you (just the repeat type)? If your annotation differs at or below the subfamily level, there may not be much you can do about ...
written 6.5 years ago by neal.platt220
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Comment: C: Differences Between Ucsc And Local Repeatmasker Results
... Is RM failing to recovering the expected repeats, or are they being misidentified. For example, are you expecting a repeat to be an ALU SINE (based on the UCSC annotation), but RM calls it a MIR, or are your RM runs not annotating the region at all? ...
written 6.5 years ago by neal.platt220
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Answer: A: Looking For Review Articles/Tutorials About Understanding And Interpreting Phylo
... It's not a review article, but the Phylogenetic Trees Made Easy book is best beginner tutorial you can get. It walks you through all the basics. I think most people can work through the book in a week or so. The third edition has ~ 200 pages. From the table of contents: Ch. 1 - Introduction Ch ...
written 6.5 years ago by neal.platt220
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Comment: C: Differences Between Ucsc And Local Repeatmasker Results
... It is very difficult to duplicate RepeatMasker results between runs. Independent runs produce similar results, but rarely are they identical. Are you using the standard RepeatMasker libraries or are you using sequences from RepBase? ...
written 6.5 years ago by neal.platt220
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Answer: A: How To Put Bootstrap And Posterior Probability Values Together In The Same Phylo
... We use Inkscape for our work. There is a small learning curve, but you can produce high-quality, publication ready images quickly. Gimp is a strong alternative as well. ...
written 6.5 years ago by neal.platt220

Latest awards to neal.platt

Good Answer 3.5 years ago, created an answer that was upvoted at least 5 times. For A: List Of Bioinformatics Books
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Question About Bwa Pe Mapping And Calling "Properly Mapping Pairs" In Samtools
Appreciated 4.8 years ago, created a post with more than 5 votes. For A: List Of Bioinformatics Books
Great Question 4.8 years ago, created a question with more than 5,000 views. For Sorting Fastq Files After Trimming (Orphans And Pe)
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Mapmi Calling Program From Subdirectory-Error Cannot Find Program In Subdirectory
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Question About Bwa Pe Mapping And Calling "Properly Mapping Pairs" In Samtools
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Error When Running Fastx (Fastx_Quality_Stats)
Popular Question 5.6 years ago, created a question with more than 1,000 views. For Csplit Multifasta File Into A *Smaller Multifasta File
Popular Question 5.6 years ago, created a question with more than 1,000 views. For Sorting Fastq Files After Trimming (Orphans And Pe)
Supporter 5.6 years ago, voted at least 25 times.
Teacher 5.6 years ago, created an answer with at least 3 up-votes. For A: List Of Bioinformatics Books
Teacher 5.6 years ago, created an answer with at least 3 up-votes. For A: Looking For Review Articles/Tutorials About Understanding And Interpreting Phylo

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