Quanyu Chen

[BUG] TypeError: Cannot read properties of undefined (reading 'sizeInBytes')

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- OS: Win11 - Extension Version: v3.18 When I exported pdf, I got some errors: ``` null ----------------------------------------------------------------------------------------- TypeError: Cannot read properties of undefined (reading 'sizeInBytes') ----------------------------------------------------------------------------------------- ``` I didn't...

**Describe the bug** A clear and concise description of what the bug is. ``` NC_000005.10:110000000-120000000 is not in /path/to/GRCh38_noY.2bit ``` **To Reproduce** I followed the instruction on the website http://genomewiki.ucsc.edu/index.php/Same_species_lift_over_construction...

Problems in chm13v2.0_RefSeq_Liftoff_v5.1.gff3

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I have used liftoff using the annotation file of GRCh38.p14 and liftoff was running normally without any problems. But when I used chm13v2.0_RefSeq_Liftoff_v5.1.gff3 (after some tests, I found it was...

racon: invalid option -- 'L'

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Hello, I am following the polishing method of Mc Cartney et al., 2022, whose doi is https://doi.org/10.1038/s41592-022-01440-3, where Racon's liftover branches were used(https://github.com/isovic/racon/tree/liftover). Here is the command: `${RACON} -t ${threads}...

gffutils database build failed with UNIQUE constraint failed: features.id

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Useful and exciting tool! But when I ran lifton with the command: ``` lifton MF2_mat.v1.0.fa ~/rawdata/GRCh38/ref/GRCh38.p14.new_name.fa -sc 0.95 -copies -g ~/rawdata/GRCh38/ref/GCF_000001405.40_GRCh38.p14_genomic.gff -polish -o CN1v1.0_mat.lifton.gff -c -cds -ad RefSeq -f type.list...

Right method to annotate genes on pangenome graph

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**PLEASE DO NOT MAKE SUPPORT REQUESTS HERE** Please the Biostars forum instead: https://www.biostars.org/new/post/?tag_val=vg Ok I will post on Biostars later. Hello dear friends! Thanks for developing vg such a useful...

How can I add an extra sequence to graph?

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Now I have a subgraph and some other sequences like other samples. I want to augment these samples to the graph to build a larger and more complete graph. How...

Now I have a full panel `APGp1 + HGSVC3 + HPRCy1`. After running the command `locityper add -d db`, I would get a reference panel to perform the LOO experiment....

Here is my command: ``` locityper add -d db -v $input.vcf -r CHM13v2.fasta -j counts.jf -L chm13v2.0_RefSeq_Liftoff_v5.1.CMRG.bed --threads 32 -e 300k ``` and I got this error: ``` [18:17:22 DEBUG]...

Aborted (core dumped)

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When I used `rpvg` to analyze my `vg mpmap` result, I got this error: ``` Running rpvg (commit: 301f553412a7f3b3c3dccad74e845868da4f0468) Random number generator seed: 1741874850 Fragment length distribution parameters found in...