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**Operating system**
Ubuntu 18.04
**Package name**
isoseq3 3.3.0 (commit v3.3.0)
lima 1.11.0 (commit v1.11.0)
ccs 4.2.0 (commit v4.2.0)
**Conda environment**
$ conda list
# packages in env…
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Hi,
I have poly(A)+ mRNA sequenced by Sequel, and aligned the iso-seq ccs reads (without polyA tail removed but with adapter removed) to the mouse reference genome. Can I consider the soft clipped…
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Hi Heng,
Can minimap2 be used to find overlaps between long RNA reads (_e.g._ PacBio Iso-seq, Nanopore 2D cDNA-seq and Direct RNA-seq reads)? Should I consider splice/junctions when I do this?
T…
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Hello Magdoll,
I have gotten an error related to the fusion transcript option (--is_fusion). I attached my log at below. Do I need to update the version? Please let me know how I can resolve this i…
tay45 updated
5 years ago
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Hello Magdoll,
I have updated the latest version of the SQANTI2. But, I can't still use the '--is_fusion'. I have downloaded it from https://github.com/Magdoll/SQANTI2. Did I download the correct o…
tay45 updated
5 years ago
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Hi, Liz:
When I run run_IceInit2.py in cDNA_Cupcake(version 6.5), I got this error:
Traceback (most recent call last):
File "MyPath/cDNA_Cupcake/build/scripts-2.7/run_IceInit2.py", line 5, in
…
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Can you give me an example on how you guys define "sequencing parameters" for `PacBio` runs?
All our runs are default, `Custom (see notes)`.
I was not able to (succesfully) apply `addSequencingPar…
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Dear @lh3 ,
We are evaluating the error-correction results of third-generation RNA reads. In the alignment results (RNA), there are too many S and H at the beginning or end of the CIGAR string. This …
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Hi,
have you used Cogent on Nanopore RNA-Seq data where the raw-read errors are ~15%? If yes, could comment on the performance of Cogent?
Thanks
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Hi,
I am new to Iso-seq and RNA-seq, now I have done PacBio Iso-Seq and alignment, how can I get -c coverage and -i identity?
Thanks a lot.