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User: Jouni Sirén

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Jouni Sirén • 90
Reputation:
90
Status:
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 Sirén • 90
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 Sirén • 90
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 Sirén • 90
0
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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 Sirén • 90
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 Sirén • 90
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 Sirén • 90

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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