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This is a question related to a strange message in the log out file after Salmon indexing on a very small genome with my own generated transcriptome and decoy.
I'm running Salmon v1.0.0 index on th…
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Hi
I am using salmon 1.2.0 to build a Salmon-SAF index on Rat data from Ensembl -- using full genome as decoy.
```
wget ftp://ftp.ensembl.org/pub/release-96/fasta/rattus_norvegicus/cdna/Rattus_…
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Hi Sergey,
I have a simulated data set that I'm using for assembler accuracy benchmarking, and Canu fails to build any unitigs from it. It's a sampling from C.elegans reference, with read lengths…
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I am using a very recent github pull of CANU (v2.0-development +312 changes (r9805 b6670537326b323d2837d7801d089f4f52b860c2)) in order to assembly our hifi pacbio data.
In terms of continuity this ve…
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Generating Contigs using UG and Reads
We would like to generate contigs using the unitigs on the dbg and the reads given as the initial input for the dbg construction. This step of the project is …
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Thanks @GuillaumeHolley and @pmelsted for such an excellent application! I have been using it for the past couple months and it has worked very well.
I just wanted to reach out to hear your thought…
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I'm mapping some long sequences (pseudo-unitigs from an assembly graph) to the human reference genome. It seems that some sequences are taking a very long time. Almost all of my runtime (>80%) is spen…
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Hi,
I'm trying to run the elastic net model implemented in pyseer on a large input file of unitigs (23.84GB), provoking the error message below. I run pyseer 1.3.3. through conda (64 bit python 3.7…
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Hi,
Is there anyway to work out which knote in the genome graph (unitigging/4-unitigger/blah.contigs.gfa) creates which contig in the final fasta.
Thanks.
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Hi,
We have some PacBio RSII targeted sequencing reads that target certain regions of an animal genome including the MHC region. Can canu be used to assemble these reads into long contigs with rea…