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The addition of this functionality is a nice inclusion in WebApollo 2 as correcting the splice junctions, with all of the concomitant joy of zooming in and out to base level takes up much of the annot…
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Too much Nodes are being merged based on SJ-only Edges:
 using STAR to the genome, and generated my BAM files. The data was from a variety of dif…
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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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Hi
I am getting an error:
make: *** No rule to make target 'sheep/data/Ovis_aries.Oar_v3.1.88.chr.gtf.mapTrans2Gene.tsv', needed by 'sheep/star/cufflinks2//pt0a.se.transcripts.riu.cufflinks2.ir…
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I need a single value for gene-level expression for each sample (or for each condition) that would be equivalent to the 'Read-pairs per sample, gene level' on the right side of the plots. Is there som…
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Hi Alex,
When I use "--outSAMtype BAM SortedByCoordinate" STAR uses only a single thread once it has started sorting, regardless of what the parameter "--outBAMsortingThreadN" is set to. This seems…
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This references #2752
I think we should strictly roll back `tophat` to Python v2.7 AND link it with `bowtie2` v2.2.5. `bowtie2` v2.3.0 was recently released, but does not play nice with `tophat` …
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Splice junctions for a certein gene locus might change among different experiment conditions, just like expression levels. For expression levels, we could use [multibigwig ](https://github.com/cmdcoli…
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Add command line functions for annotating exons next to splice junctions, creating SE and MXE events, and calculating psi