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jcvi.graphics.ribbon module is a modified version of the synteny module which allows plotting of arbitrary alignments and multiple genomic feature tracks. Ribbon plots are not based on ortholog linkag…
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When I run the following command:
STAR --runThreadN 1 --runMode alignReads --genomeDir ~/genomics/yeast_genome_index_3 --readFilesIn SC_WT_glycerol_1.fastq
or
STAR --runThreadN 1 --runMode alignRea…
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Hey there,
I am trying to create a dotplot of an alignment I made with minimap, I converted the minimap output (sam format) to a paf format and
tried running dotplotly on it to visualize the outpu…
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Hi,
I ran multiple whole genome alignments using cactus to generate the hal file, and ran the "cactus-hal2maf js_hal2maf evolver27species.hal evolver27species.maf.gz --refGenome xxxx --chunkSize 50…
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Hi,
I am using PASA as part of my genome annotation pipeline.
Despite the good quality of the input Trinity assembly( > 90% busco),
the final PASA result is very bad (13% busco).
I ran PASA bo…
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I hacked together a method based on the minimap2 alignment strategy. The basic idea right now is that after producing whole genome alignments via minimap, one can use the paftools liftover command to …
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I have been [told by Ensembl](https://github.com/Ensembl/ensembl-vep/issues/1053#issuecomment-924650545) that:
> Ensembl transcripts completely match the reference genome they are annotated against…
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Hi,
I am getting following error when selected gmap only with sample data provided with pasapipeline as well as my own data as well. I used updated version of gmap.
-connecting to MySQL db: rice_p…
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Hi
I have a question on the MAFindex module in biopython. I'd like to extract single base alignments of one specific target genome from a database of multiple genome alignments using the maf indexing…
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**Description:**
We are trying to visualize the reads from SARS CoV2 samples on the gnome terminal. Upon uploading the sample file we see the following error.
> **Error encountered querying alignm…