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circompara2 is using tophat, star and bowtie2. why all three? I mean is it necessary to run all three or One of them is enough ???
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We’ve been getting some odd results in a single cell study and tracked these down to a set of genes which had odd clusters of mapped regions over only part of one exon of the gene.
When we looked at …
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- [x] ⚒ Tear out EF
- [x] 🏫 Identify candidates
- [x] 👷 Try out candidates in a sandbox
- [x] :tophat: Make final decision
Currently thinking SQLite + Dapper (or some other micro ORM).
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I was running spectramerge and I found this error that lead to no output file being created. It looks like an unhandled cvParam stopped the writing of the output file. This file worked on the smoot…
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Determine if Jenkins AMI exists and it’s the correct version; otherwise, it will launch Packer. Jenkins is maintained in https://github.com/stelligent/tophat
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Hello,
I have an issue in running TopHat2 on a set of strand specific single end reads on the mouse genome (mm10). Basically, the TopHat analysis (I used both TopHat 2.0.13 and 2.1.0) gets stuck at t…
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use the tophat junctions.bed files as the interval for the RNA-seq analysis #maketracktable
displayMode="COLLAPSED"
![igv_snapshot4tracktable](https://cloud.githubusercontent.com/assets/13783075/2…
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I took a 150kb region from _H. saltator_ and simulated Illumina reads from the transcripts encoded in that region. The idea was to use the data for instruction: teach the students basic RNA-seq analys…
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**Is your feature request related to a problem? Please describe.**
I have z-scores in my column data which I would like to display in the reduced dimension panel. Sometimes the distribution of thes…
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Hi, maybe I missed this, but which aligner is recommended ? STAR or Tophat, or bwa, bowtie2 etc.
Thanks,
Colin