User: chenyangkang24

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Posts by chenyangkang24

<prev • 8 results • page 1 of 1 • next >
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Answer: A: Calculate effective population size (Ne)
... I think that's currently inapplicable and does not make sense theoretically. Maybe multi-individuals make sense. ...
written 15 days ago by chenyangkang240
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Comment: C: BWA error: no ID within the read group line
... Thank you anyway for the suggest ...
written 18 days ago by chenyangkang240
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Comment: C: BWA error: no ID within the read group line
... Well that didn't work for me. I think we face different issue. In your case, maybe you can try `'@RG\tID:{1}\tSM:{1}\tLB:{1}'` as well? ...
written 18 days ago by chenyangkang240
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Comment: C: CodeML Troubleshooting Help
... Oh my god that's the point. I did orthologs codon-alignment which gives me the information of frame shift mutation in as sign "!", and I just convert the alignment to phylip fortmat and pass it to codeml. I think something's gonging wrong with the convertion, to deal with the "!", result in erro len ...
written 18 days ago by chenyangkang240
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bwa read group tagging failed in PBS cluster
... Hi guys, I was trying to build a PBS script for bwa alignment (reads mapping) and submit it to the PBS cluster, but failed with this: ``` [E::bwa_set_rg] no ID within the read group line ``` my code: >bwa mem -t 20 -R '@RG\tID:NL\tSM:NL\tLB:NL\tPL:Illumina' reference.fasta 1.fastq.clean.gz 2.f ...
software error alignment next-gen written 19 days ago by chenyangkang240
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Comment: C: VCFtools filtration strategy --hwe
... Thank you, That's exactly what I thought. I asked this "stupid" question because some tutorial add this option without explanation, even if the samples comes from different species. In this case many SNPs were gone. Yangkang ...
written 19 days ago by chenyangkang240
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Comment: A: BWA error: no ID within the read group line
... I met the same error when send this to PBS. I think something's going wrong with the quote, or @, or some special letter that PBS cannot recognize. ...
written 19 days ago by chenyangkang240
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VCFtools filtration strategy --hwe
... Hi everyone, I'm currently confused by the option of VCFtools: --hwe. From my understanding, this option measure whether each site from every individual in the VCF file significantly departures from the HW balance. But what if individuals in the file are not from the same population or even species ...
genome next-gen snp sequencing written 22 days ago by chenyangkang240 • updated 22 days ago by pufferfish290

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