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I have mapped alignments with STAR (stranded data, dUTP, PE101), that lack the XS flag. I guess that is reason why assembly step fails:
```
java -Xmx6g -jar ~/bin/IsoSCM-2.0.9.jar assemble -bam WT.ba…
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I'm trying to perform 2-pass mapping on some canine RNA-seq libraries (STAR v2.4.1d). When I tested with one sample, everything worked fine. However, now that I'm extending to the entire cohort (29 sa…
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Hi,
It seems we could merge these 2 terms:
RNA splicing factor activity, transesterification mechanism ; GO:0031202
spliceosomal catalysis ; GO:0000385
They're essentially the same thing. Basicall…
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I am was running enumerate in relatively large datasets (~30GB bam), with -max_isoforms 20, but had to kill the job because it was generating >1TB isoforms.gtf. Is this to be expected and should -max_…
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Hi @cdeboever3 I just installed all the prerequisites and when trying to download the data I get this error:
$ ipython ext_data.ipynb --pylab inline
WARNING: 'inline' not available as pylab backend, …
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To support explicit splice declaration it is proposed that CIGAR operators be added to support canonical, non-canonical, major, minor and potentially other types of splices. This issue is to discuss …
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I am using stringtie 1.0.2 on a ubuntu server, which has 32GB memory and 32GB swap, 8 core cpu. When I am processing a bam file generated by HISAT, the stringtie process always be killed by linux kern…
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Hi,
I am trying to create a compound node and move some elements to that compound node by using eles.move( ) function. I observed that when width or height attribute is set for nodes, eles.move( ) …
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VectorBase reported:
We encountered the problem that using gff3 submissions from the community included some which visually looked fine but subsequently after export and processing contained in-frame …
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Hi Alex,
I am preparing STAR for use and getting this failure on genomeGenerate. I've tried twice, the second time adding `--limitGenomeGenerateRAM 30000000000` but this doesn't seem to help. It fail…