User: StarCute

gravatar for StarCute
StarCute110
Reputation:
110
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Trusted
Location:
United States
Last seen:
1 year, 7 months ago
Joined:
3 years, 8 months ago
Email:
c******@rams.colostate.edu

Posts by StarCute

<prev • 15 results • page 1 of 2 • next >
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Comment: C: Abyss assembler hangs
... Yeah. For some reason the assembler works fine if I just set the variable **j** (number of threads), but when I include the **np** (number of MPI processes) as well, it fails. ...
written 23 months ago by StarCute110
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Comment: C: Abyss assembler hangs
... 512GB RAM and kmer 96 ...
written 23 months ago by StarCute110
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Abyss assembler hangs
... Hey, I'm using abyss version 2.0.2 and am unable to run an assembly to completion. I am running on a Ubuntu 16.10 server with a small (~1 GB dataset) with a small k (<=96). I have tried the solutions suggested in [this][1] and [this][2] post, but the assembly continues to hang during the **Findi ...
assembly abyss written 23 months ago by StarCute110 • updated 21 months ago by Biostar ♦♦ 20
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CWL Argument Error
... I have a cwl file: cwlVersion: cwl:draft-3 class: CommandLineTool baseCommand: [bwa, mem] inputs: - id: reference type: File inputBinding: position: 1 - id: forward type: File inputBinding: position: 2 - id: sam ...
software error cwl written 2.2 years ago by StarCute110 • updated 23 months ago by karl.nordstrom80
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Comment: C: Trouble compiling ABySS from source
... Install the required [dependencies][1] mentioned in the documentation. [1]: https://github.com/bcgsc/abyss#install-abyss-on-debian-or-ubuntu ...
written 2.3 years ago by StarCute110
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SNP Filtering Metrics from VCF
... I have two VCF files. One was generated using Samtools mpileup and the other Freebayes. I would like to do an intersection of these two VCF files and combine them using VCFtools. I want to filter SNPs based on their quality score, but do not know of a good way to choose the quality score value to fi ...
snp written 2.5 years ago by StarCute110 • updated 2.4 years ago by vchris_ngs4.5k
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Comment: C: Identifying mate pair reads from SAM file without using QNAME
... I'm worried about one SAM file having the 0/1, 0/2 format and another having an identical QNAME format.    QNAME_0/1 QNAME_0/2 OR QNAME QNAME ...
written 2.7 years ago by StarCute110
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Identifying mate pair reads from SAM file without using QNAME
... I am writing a C++ program that needs to process mate pair reads. I would like to avoid using the QNAME field in combination with the FLAG and PNEXT fields. I'd prefer not using the QNAME because the format seems to change depending on how the data was processed. Is it sufficient to simply check the ...
alignment written 2.7 years ago by StarCute110 • updated 2.7 years ago by Devon Ryan85k
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Answer: A: How to interpret positive and negative POS values in alternative alignment field
... Following the advice given from Brian Bushnell and Istvan Albert, I was able to find the block of code that produce the multiple hits. Under bwa/bwase.c, beginning at line 467, we can see that, in fact, the '+' and '-' signs refer to the positive and negative strands.       ...
written 2.9 years ago by StarCute110
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Comment: C: How to interpret positive and negative POS values in alternative alignment field
... I'd like to assume that it refers to the positive and negative strand, but I can't find anything confirming that. ...
written 2.9 years ago by StarCute110

Latest awards to StarCute

Popular Question 2.8 years ago, created a question with more than 1,000 views. For How does kmer length affect total assembly size?
Scholar 2.9 years ago, created an answer that has been accepted. For A: How to interpret positive and negative POS values in alternative alignment field
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: How to interpret positive and negative POS values in alternative alignment field
Student 3.5 years ago, asked a question with at least 3 up-votes. For How does kmer length affect total assembly size?

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