User: benv

gravatar for benv
benv480
Reputation:
480
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Trusted
Location:
Canada
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2 days, 17 hours ago
Joined:
2 years, 5 months ago
Email:
b***@bcgsc.ca

Posts by benv

<prev • 62 results • page 1 of 7 • next >
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Comment: C: Rescaffolding a genome assembly?
... Thanks for posting the update -- I'm interested to hear how it goes for you! ...
written 2 days ago by benv480
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Comment: C: Rescaffolding a genome assembly?
... There's nothing in the ABySS toolset for identifying/cutting misassemblies, unfortunately. I noticed that there is a tool called [NxRepair][1] that detects/cuts misassemblies using mate pair reads, but I have not tried it. [1]: http://nxrepair.readthedocs.io/en/latest/tutorial.html ...
written 5 days ago by benv480
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Comment: C: abyss fixmate error (but read IDs seem appropriate)
... See the abyss-pe man page (available in the `doc` subdirectory in the source tarball) for more info about `abyss-pe` parameters. From the root of the ABySS source tree, you can view it by running 'man doc/abyss-pe.1'. ...
written 16 days ago by benv480
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Answer: A: abyss fixmate error (but read IDs seem appropriate)
... Hi @jdoyle30724, You have the right idea, but `abyss-pe` is getting confused because "pe" is a reserved variable. Try changing "pe" => "pet" in your command and it should work: for k in `seq 41 10 81`; do mkdir k$k abyss-pe -C k$k lib='pet' mp='mp' np=48 j=24 name=test k=$k ...
written 16 days ago by benv480
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Comment: C: Reading single-end reads takes forever
... Good. Glad to hear that! ...
written 7 weeks ago by benv480
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Answer: A: Reading single-end reads takes forever
... Hi @RoseString, Thanks for providing so many details about your assembly job and in such a nicely organized format. It really saves time and helps me to understand what is going on. The `se=...`, `pe=...`, `mp=...`,`in=...`,`lib=...` parameters are a frequent point of confusion for ABySS users, un ...
written 8 weeks ago by benv480
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Comment: C: Abyss-fixmate: error: all reads are mateless
... I see. Those read IDs do not follow the rules I described above. For example, the read IDs for the first pair of reads need to be either: `@SRR960028.1` (read 1 file) and `@SRR960028.1` (read 2 file) OR `@SRR960028.1/1` (read 1 file) and `@SRR960028.1/2` (read 2 file) You will have to fix the I ...
written 9 weeks ago by benv480
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Comment: C: Abyss path subprograms
... Yep, as far as I understand it is basically an overlap parameter. And setting -k == -m would probably work. Good point about the coverage info. As far as I know, the ABySS tools don't strictly require the coverage values to be present in the FASTA headers, so you should still be able to get the t ...
written 9 weeks ago by benv480
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Answer: A: Abyss path subprograms
... That is a good question, Damian. (I have sometimes wondered about that myself.) One thing I can tell you that `k` is indeed used by the downstream ABySS programs. For example, AdjList finds end-to-end sequence overlaps of `k-1` or lower to build the compacted de Bruijn graph. In general, `k` doe ...
written 9 weeks ago by benv480
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Answer: A: Abyss-fixmate: error: all reads are mateless
... Hi @jozs2019, It is most likely a read naming issue that is preventing the reads from being properly paired by ABySS. (I can confirm this if you post the first 10 lines of your read 1 and read 2 files. You can use a gist if you like.) ABySS requires that the FASTQ IDs (i.e. the first whitespace ...
written 9 weeks ago by benv480

Latest awards to benv

Teacher 15 days ago, created an answer with at least 3 up-votes. For A: regenerating -contigs file in ABySS
Appreciated 8 weeks ago, created a post with more than 5 votes. For A: Reading single-end reads takes forever
Scholar 8 weeks ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: regenerating -contigs file in ABySS
Scholar 9 weeks ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Scholar 9 weeks ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Scholar 9 weeks ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
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