User: DoubleDecker

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DoubleDecker140
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140
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United Kingdom
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1 year, 5 months ago
Joined:
6 years, 2 months ago
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Posts by DoubleDecker

<prev • 30 results • page 1 of 3 • next >
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Comment: C: dealing with unknown base pairs after assembly
... N is a IUPAC code for an unknown base, and Xs are probably masked bases but you need to check the documentation of your program to confirm this... ...
written 4.3 years ago by DoubleDecker140
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Comment: C: "An Explosion Of Bioinformatics Careers" - from Science Careers
... I think high-throughput methods are employed in pretty much every research group now, which was not the case in the past, so there is definitely more demand for bioinformatics skills within your average Biology department. ...
written 4.3 years ago by DoubleDecker140
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Comment: C: dealing with unknown base pairs after assembly
... You asked "how can I deal with these unknown base pairs". The bottom line is you do not have to deal with them, most downstream tools can deal with them. It is common to have many Ns in assemblies. ...
written 4.3 years ago by DoubleDecker140
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Comment: C: How to determine the ancestral state of a site in the outgroup?
... No, non-model species. ...
written 4.3 years ago by DoubleDecker140
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Comment: C: dealing with unknown base pairs after assembly
... Most downstream tools will know how to handle these unknowns, so should not be a problem to just leave them there. ...
written 4.3 years ago by DoubleDecker140
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How to determine the ancestral state of a site in the outgroup?
... I have generated transcriptomes from my focal species and its outgroup. I want to now find out what is the ancestral state at some sites based on the outgroup. How do people usually accomplish this? The easiest way to do this would be to map the outgroup reads to the focal species transcriptome but ...
alignment snp written 4.3 years ago by DoubleDecker140
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Comment: C: Soft-Clipping And Variant Calling
... Yes, that's what I meant. I did not use the option to output alternative alignments in BWA mem. ...
written 4.6 years ago by DoubleDecker140
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Comment: C: Soft-Clipping And Variant Calling
... That's really great, will save me a lot of disk space not to prepare yet another set of bam files. EDIT . OK, I am scratching my head right now... so you only got only 5 additional SNPs having added an identical string to all the reads? But it seems to me you assigned low Phred quality values (2) t ...
written 4.6 years ago by DoubleDecker140
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Soft-Clipping And Variant Calling
... Having aligned my reads with BWA-mem, I noticed that a lot of alignments are dodgy, to put it mildly, e.g. with both ends massively soft-clipped. I now wonder if I need to filter my alignments to get rid of such soft-clipped alignments before performing variant calling or (preferably!) variant calle ...
gatk bwa written 4.6 years ago by DoubleDecker140 • updated 4.6 years ago by Mick0
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Comment: C: Do We Have A Read Expression Summarization Tool For Bwa?
... Well, yes, I ran samtools and express on the same input file. In fact, I had a look at express mailing list where they admit that express is not compatible with BWA yet. You can find a script there which should be able to convert bwa-aln output to bowtie output and thus work with both RSEM and expre ...
written 4.6 years ago by DoubleDecker140

Latest awards to DoubleDecker

Great Question 4.0 years ago, created a question with more than 5,000 views. For Counting Number Of Bases In A Fastq File
Epic Question 4.0 years ago, created a question with more than 10,000 views. For Counting Number Of Bases In A Fastq File
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Detecting Chimeric Transcripts In Rna-Seq De Novo Assemblies
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Does Order Within Read Pairs In Interleaved Files Matter?
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Getting Blastx Translated Query
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Soft-Clipping And Variant Calling
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Detecting Chimeric Transcripts In Rna-Seq De Novo Assemblies
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Counting Number Of Bases In A Fastq File
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Counting Number Of Bases In A Fastq File
Appreciated 4.6 years ago, created a post with more than 5 votes. For A: How To Get Domain Name Or Family Name Of A Interpro Domain Using Ipr Id
Good Answer 4.6 years ago, created an answer that was upvoted at least 5 times. For A: How To Get Domain Name Or Family Name Of A Interpro Domain Using Ipr Id
Teacher 4.6 years ago, created an answer with at least 3 up-votes. For A: How To Get Domain Name Or Family Name Of A Interpro Domain Using Ipr Id

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