User: benv

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benv430
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430
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Location:
Canada
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3 days, 4 hours ago
Joined:
2 years, 4 months ago
Email:
b***@bcgsc.ca

Posts by benv

<prev • 58 results • page 1 of 6 • next >
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Comment: C: Reading single-end reads takes forever
... Good. Glad to hear that! ...
written 20 days ago by benv430
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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 26 days ago by benv430
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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 4 weeks ago by benv430
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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 4 weeks ago by benv430
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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 4 weeks ago by benv430
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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 4 weeks ago by benv430
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Answer: A: Abyss-map complains 'missing arguments'
... This type of error (`abyss-map` missing arguments), is usually caused by a problem with how the input files are specified. In this case, `abyss-pe` is having trouble because `pe` is a reserved variable, but you are using it like a user-defined variable. You could fix the problem by changing `lib=' ...
written 4 weeks ago by benv430
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Answer: A: abyss-pe without openmpi
... Hi Vinay, Sorry! Yesterday (in another thread) I suggested adding `np=1` to your `abyss-pe` command. But looking at `abyss-pe` script, I see that won't work for running ABySS without MPI. `abyss-pe` tries to detect the number of cores available based on the environment variables set by your job s ...
written 8 weeks ago by benv430
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Answer: A: ABySS error: sequence and quality must be the same length near ...
... FASTQ records consist of 4 lines each. The first line is the header and contains the read ID. The second line contains the sequence. The third line is just a "+". The fourth line is the quality score string. Each character in the quality score string encodes quality score for the corresponding ...
written 9 weeks ago by benv430
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Comment: C: installing ABYSS using cygwin
... Fair enough. I will need you to provide some more detailed information before I can help, though. At what step did the commands fail? What was the error message? Was there partial output from the failed command? ...
written 8 months ago by benv430

Latest awards to benv

Appreciated 26 days ago, created a post with more than 5 votes. For A: Reading single-end reads takes forever
Scholar 26 days ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Teacher 26 days ago, created an answer with at least 3 up-votes. For A: regenerating -contigs file in ABySS
Scholar 4 weeks ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Scholar 4 weeks ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Scholar 4 weeks ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: regenerating -contigs file in ABySS
Scholar 14 months ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Scholar 16 months ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Scholar 17 months ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Scholar 18 months ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Scholar 18 months ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: regenerating -contigs file in ABySS
Scholar 19 months ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: regenerating -contigs file in ABySS
Scholar 2.1 years ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: regenerating -contigs file in ABySS

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