User: Jouni Sirén

gravatar for Jouni Sirén
Jouni Sirén90
Reputation:
90
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Trusted
Location:
UCSC Genomics Institute
Website:
https://iki.fi/jouni.s...
Twitter:
jltsiren
Last seen:
7 hours ago
Joined:
10 months, 2 weeks ago
Email:
j*******@gmail.com

Posts by Jouni Sirén

<prev • 6 results • page 1 of 1 • next >
3
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Answer: A: Best way to obtain reference and non-reference k-mer
... The easiest way is probably doing it outside vg: 1. Extract all kmers (kmer occurrences) with `vg kmers`. 2. Extract the selected paths in FASTA format with `vg paths -v graph.vg -F -p path-names.txt > output.fa`. 3. Determine the kmers in the paths using an external tool. 4. Compare the kmer se ...
written 26 days ago by Jouni Sirén90
1
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Answer: A: Vg gamsort temporary folder
... `vg gamsort`, as well as most other vg commands, takes the temporary directory from environment variables. The primary variable is `TMPDIR`, but vg also checks a number of other variables (`TMP`, `TEMP`, `TEMPDIR`, `USERPROFILE`) if that has not been set. If everything else fails, vg falls back to ` ...
written 26 days ago by Jouni Sirén90
2
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Answer: A: Extract linear representation of paths in VG graph
... You can use `vg paths -F` to extract entire paths in FASTA format. By default, this extracts all paths in the graph. You can use option `-p FILE` to specify a list of path names in a file and option `-Q PREFIX` to extract all paths with the given name prefix. In order to extract subpaths, you can c ...
written 4 months ago by Jouni Sirén90
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Comment: C: More haplotype threads than expected
... Sometimes haplotypes contain alternate alleles of overlapping variants that make no sense together (under the vg interpretation of the VCF). By default, this causes a phase break in GBWT construction. With option `-o`, the construction will use the reference allele for the variant that occurs later ...
written 7 months ago by Jouni Sirén90
1
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Answer: A: Error in vg : vg Assertion `reference_for.count(fasta_contig)' failed.
... Your VCF and reference files are probably using different contig names. If so, you can match them by adding options `-n vcf_contig=fasta_contig` (e.g. `-n chr1=1 -n chr2=2`) to the `vg construct` command. ...
written 8 months ago by Jouni Sirén90
2
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Answer: A: How much memory do we need for pruning a variation graph of a chromosome?
... The memory usage is effectively unlimited in v1.19.0. It will be far more reasonable in v1.20.0, and the changes are already included in the master. The `vg prune` subcommand enumerates all 24 bp paths in the graph. If the path makes > 3 edge choices, vg stores the edge that violated the constra ...
written 10 months ago by Jouni Sirén90

Latest awards to Jouni Sirén

Scholar 26 days ago, created an answer that has been accepted. For A: Extract linear representation of paths in VG graph
Scholar 26 days ago, created an answer that has been accepted. For A: Vg gamsort temporary folder
Teacher 26 days ago, created an answer with at least 3 up-votes. For A: Best way to obtain reference and non-reference k-mer
Scholar 4 months ago, created an answer that has been accepted. For A: Extract linear representation of paths in VG graph

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