User: carolina.santiago.t

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Posts by carolina.santiago.t

<prev • 10 results • page 1 of 1 • next >
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Error estimating covariance matrix and individual admixture proportions
... Hi, I am trying to perform a PCA with some strains whole-genome NGS data. When i run the command: `python pcangsd.py -beagle name.beagle.gz -admix -o name_test -threads 10,` I obtain `"ValueError: k must be greater than 0."` Can someone help me understand what I am doing wrong? Thanks in advance! ...
pca pcangsd written 5 weeks ago by carolina.santiago.t0 • updated 13 days ago by Sej Modha4.7k
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Comment: C: BAM index via samtools
... Thank you, once again, for your help! I am really sorry but my question was the result of a mistake, that i only realysed now. I was using the computer at distance, i don't know if it was some kind of delay but the truth is that now i'm looking at the same files at the computer and they do have the ...
written 8 weeks ago by carolina.santiago.t0
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Comment: C: BAM index via samtools
... Thank you for your help! I can't understand why, when using the same input file and the same command, the size of the output can be different. That´s messing with my head. Do you know the reason why this happens? ...
written 8 weeks ago by carolina.santiago.t0
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BAM index via samtools
... In order to use genomic data in IGV I converted SAM files to BAM and them executed the index via samtools. I observed that when generating the index from the same BAM file the output could have different sizes. To test I inputed the same genome three times, with diferent index in IGV and verified sl ...
genome assembly next-gen written 8 weeks ago by carolina.santiago.t0
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Understanding a blast output
... I performed a genome blast and saved the results for each chromosome in a .xml file. For each gene, 5 hitlist_size were defined. In the xml output file in the end of those 5 hits there is a section. Can anyone help me understand the meaning of this section please? Below, there is an exemple of the ...
xml blast written 11 months ago by carolina.santiago.t0 • updated 11 months ago by lakhujanivijay5.0k
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(Closed) Understanding a blast output
... `enter code here`I performed a genome blast and saved the results for each chromosome in a .xml file. For each gene, 5 hitlist_size were defined. In the xml output file in the end of those 5 hits there is a section. Can anyone help me understand the meaning of this section please? Below there is a ...
xml blast written 11 months ago by carolina.santiago.t0
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Comment: C: Creation of a VCF file from scratch with python
... Thank you! I will try this. ...
written 15 months ago by carolina.santiago.t0
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Comment: C: Creation of a VCF file from scratch with python
... I want to create a header that allows me to save some data that is not in the template CSV. So i want either to create a new CSV that i can use to save those fields or to manipulate a template in order to add those. ...
written 15 months ago by carolina.santiago.t0
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Comment: C: Creation of a VCF file from scratch with python
... I want to create a header that allows me to save some data that is not in the template CSV. So i want either to create a new CSV that i can use to save those fields or to manipulate a template in order to add those. ...
written 15 months ago by carolina.santiago.t0
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Creation of a VCF file from scratch with python
... Hello! I want to make a VCF file with a header line syntax like "#CHROM POS REF ALT". Is it possible to create such a VCF file from scratch with python? Thanks in advance ...
vcf python written 15 months ago by carolina.santiago.t0 • updated 15 months ago by finswimmer13k

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Popular Question 10 months ago, created a question with more than 1,000 views. For Creation of a VCF file from scratch with python

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