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Create a master workflow (and run it) that needs only the NCBI Accession numbers (listed as SRA-runtable.csv) that uses the *Open2C ecosystem* outputs the .cool file of the interaction matrix - or at …
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Hello, I am currently using the test.gfa file you provided to reproduce the results. However, when using the Dfam TE tools, I am unsure which dataset from the famdb library to use for comparison and c…
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Hi,
I've discovered an edge case issue where `prep_rnaseq_alignments_for_genome_assisted_assembly.pl` fails by trying to create a symlink to `prefix.bam.norm_200.bam` in a directory where it alrea…
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Hi there,
I apologize for the naive question I'm about to ask, but I've been struggling with this for a week and would appreciate some help. I created a custom gene index using a FASTA file of fusi…
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In some cases, I believe that the "View chimeric alignments in split screen" feature is zooming to the wrong endpoint on the supplementary read. Here is an example:
### Other workflow execution
_No …
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Dear Brian
I have a problem about mapping and aligning transcripts to the genome using PASA. Can the transcript here be a non-coding transcript? My purpose is to verify the GT-AG rule for non-coding …
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Hi
In the Cactus paper (https://www.biorxiv.org/content/10.1101/730531v3) it mentions that it expects the input genomes to be soft-masked. I was wondering how Cactus treats the soft-masked regions.…
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From igv-help group...
Hi,
We are trying to visualize bams generated by minimap2, run as part of the dipcall pipeline (https://github.com/lh3/dipcall), for the Genome in a Bottle HG002 Q100 T2T a…
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I was trying to run sniffles in a workflow, where the alignments and variant calls are done on separate VMs.
I get an error that it can't find the genome.fa file (gives the path from the alignmen…