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Does suppa2 apply to pacbio iso-seq ?
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Dear SPAdes team,
I am a bit puzzled about the best practice for the hybrid rnaSPAdes algorithm, when used with PacBio IsoSeq long reads and Illumina short reads.
Form the different spades manua…
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Hello, I am following the [preprocessing notebook](https://github.com/YosefLab/Cassiopeia/blob/refactor/notebooks/preprocess.ipynb) in the refactor branch with my own GESTALT data. I believe it has be…
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Hi there,
I am trying to use PASA to produce a genome annotation, based solely on transcript sequence alignment (i.e no preexisting gene models). The output I'm looking for is a gff with gene, mRNA, …
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Hello, thanks for this fantastic software.
I subscribe to kottke.org and noticed this issue in the iOS app:
`[visualcapitalist.com]` is showing up as `[visualcapitalist.com.-com]`
Same wi…
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Hi again @mattjones315, I wanted follow up on the missing data issue that we discussed in issues #110 and #126. I went through the `allele_table` generated from my GESTALT data and counted up the numb…
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Since early 2018 @wfcooke has had to revert commits 48e90d0b928457e64c80b065c32f1131cc6b6dfb and bc6c6e65d658f7cdddf0c589ae770feb40287c01 to recover solutions in the SPEAR model. The first commit incr…
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Hello Brian,
I am trying to launch STAR-Fusion for de novo reconstruction of fusion transcripts using the Trinity docker, and I’m getting errors about genome_lib_dir location. Below the steps I fol…
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Hi Liz,
I'm working through reconstruct_contigs.py as part of Cogent v6.1.0 to eventually collapse my isoseq transcripts. I started with just under 15k transcripts as input which generated 1,811 pa…
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Hi Sebastian,
Hope all is well. As you already know, we're using Arriba in our pipeline and the more gene fusions data we gather through processing, the more questions we raise :]
We see that fo…