User: cts

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cts1.5k
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Pasadena
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http://ctskennerton.gi...
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Posts by cts

<prev • 108 results • page 2 of 11 • next >
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Answer: A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
... I also fails to install on a linux server running RHEL, which has by default a pretty old version of gcc (4.4.7). I've tried to install a local and updated version of gcc (4.6.3) however there is something about your make files that don't recognize a non-standard location for g++. For example: $ w ...
written 3.0 years ago by cts1.5k
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Answer: A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
... I tried to install just now on my iMac 10.9 using clang 5 and I get a number of errors related to the tr1 namespace. It would appear that on my system this namespace and the tr1 header files don't exist. Perhaps there is a robust solution that you can implement in the cmake configuration to deal wit ...
written 3.0 years ago by cts1.5k
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Answer: A: NCBI BLAST+ installation problems?
... It's not an installation error, it is a runtime error. You will probably have to contact the blast support page directly for the NCBI to look into it ...
written 3.1 years ago by cts1.5k
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Answer: A: Align short reads to multiple reference sequence
... These programs are designed to give only a single alignment. If you want alignments from all of your query sequences onto your database you could just use blast. Alternatively bowtie can also give you all alignments with the -a option; check out the manual http://bowtie-bio.sourceforge.net/manual.sh ...
written 3.1 years ago by cts1.5k
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Answer: A: Orientation in paired-end sequencing?
... In Illumina paired-end sequencing the two two mates will be sequenced in the opposite direction to one another (see my ASCII art below), so what you expect from this is that the reads should be pointing into each other, which would be the expected orientation. The reads can be in other orientations ...
written 3.2 years ago by cts1.5k
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Answer: A: [samtools reheader] Can't change chromosome name
... My guess would be that samtools reheader outputs a bam file which is a binary representation of the text from a sam file. That is why you're getting all those unreadable characters on your screen. To test this out try to redirect the output to a file and then use samtools view to see the text repres ...
written 3.2 years ago by cts1.5k
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Answer: A: Average nucleotide identity
... The species boundary is 94-95% depending on the reference you choose. Other boundaries such as genus and family have also been done using AAI (average amino acid identity). Check out the following references: Richter M, Rossello-Mora R (2009) Shifting the genomic gold standard for the prokaryotic ...
written 3.2 years ago by cts1.5k
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Answer: A: How to detect rRNA from reads ?
... I've used SortMeRNA with good effect before.  ...
written 3.3 years ago by cts1.5k
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Answer: A: how to extract those reads which mapped at 1kb of specific location on chromosom
... You can make a bed file for your coordinates of interest and then use the -L option in samtools view to extract the reads from your region of interest. ...
written 3.3 years ago by cts1.5k
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Answer: A: Interactive Perl Learning
... I used this site when I was first learning a language. It single-handedly got me into bioinformatics http://www.woolfit.net/perl/classindex.html  ...
written 3.3 years ago by cts1.5k

Latest awards to cts

Good Answer 2.8 years ago, created an answer that was upvoted at least 5 times. For A: How To Annotate A Newly Sequenced Genome
Scholar 2.8 years ago, created an answer that has been accepted. For A: [samtools reheader] Can't change chromosome name
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: How To Annotate A Newly Sequenced Genome
Scholar 3.0 years ago, created an answer that has been accepted. For A: [samtools reheader] Can't change chromosome name
Centurion 3.0 years ago, created 100 posts.
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: How To Identify The 16S Rrna Gene Sequence In A Genome
Scholar 3.2 years ago, created an answer that has been accepted. For A: [samtools reheader] Can't change chromosome name
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Command Line Program For Constructing Phylogeny Tree In Minutes (500 Sequences)?
Scholar 3.2 years ago, created an answer that has been accepted. For A: [samtools reheader] Can't change chromosome name
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Command Line Program For Constructing Phylogeny Tree In Minutes (500 Sequences)?
Guru 3.3 years ago, received more than 100 upvotes.
Appreciated 3.3 years ago, created a post with more than 5 votes. For A: How To Annotate A Newly Sequenced Genome
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Command Line Program For Constructing Phylogeny Tree In Minutes (500 Sequences)?
Supporter 3.4 years ago, voted at least 25 times.
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Command Line Program For Constructing Phylogeny Tree In Minutes (500 Sequences)?
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Compare A Denovo Assembly To The Reference Genome
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: Is Igv Software The Only Available Software To Open Bam File
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: What Does It Mean To Find The Intersection, Complement And Union Of .Vcf Files?
Teacher 4.1 years ago, created an answer with at least 3 up-votes. For A: Creating A Phylogenetic Tree From A Multiple Sequence Alignment.
Appreciated 4.2 years ago, created a post with more than 5 votes. For A: How To Annotate A Newly Sequenced Genome
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: How To Annotate A Newly Sequenced Genome
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: How To Identify The 16S Rrna Gene Sequence In A Genome
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: How To Extract All The Gene Names From A Chromosomal Region In Ensembl Using Pyc

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