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Hello,
I have had a problem trying to use biopython/Bio/AlignIO/MafIO.py recently
Version: Cloned from Github repository Feb 14 2017
In particular, I have been having problems using the 'get_…
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From Vivek Krishnakumar,
> As Colin chimed in, yes this is definitely a useful feature to have in WebApollo, which is why we implemented it at the WebApollo hackathon last year (Jun 2014).
> My imple…
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Redundancies with bowtie, bowtie2
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Hi,
I have run the IsoSCM (version 2.0.11) tool using the following command.
java -Xmx2048m -jar IsoSCM-2.0.11.jar assemble -bam simulated_mapped_read.sorted.bam -base simu_tool -s reverse_forward
B…
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hello,
I used MiXCR for Illumina PE data from human TCR. I have two questions about the result.
1. The two analysis results were not consistent with same command lines. I followed the tutorial from ur…
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I am using Hisat2/Stringtie to assemble a set of reference annotations from multiple libraries. I am following the procedure laid out on the Stringtie website.
Some of the libraries were created wit…
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Submitter: Scott Labrozzi
Email: scott.labrozzi@mlb.com
A question on recommendations:
Video and audio segment end times will not be the same (i.e. a/v AUs are essentially different durations) thus t…
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I am evaluating HISAT2 and other aligners using simulated reads. I see numerous cases where HISAT2 picks the incorrect alignment even when the fragment size is much larger than the max specified by -X…
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Currently, STAR only uses intron motif information to determine the strand output in the XS tag. Other aligners (TopHat, HISAT) allow library information to be explicitly specified. When aligning read…
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#### TODOS (again):
- [x] re-branch (client-side port?), jbrowse and Apollo
- [x] finish porting MultisequenceProjection to shared
- [x] remove back-end projection sequences
- [x] pull scaffold sequen…