User: Floydian_slip

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Floydian_slip130
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Posts by Floydian_slip

<prev • 59 results • page 1 of 6 • next >
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Comment: C: Is reusing a subset of features in another layer of classification wrong or over
... Thanks, Mensur. I do realize that this is not over-fitting in the strict sense of the word. My main concern is: can this approach be criticized and be found inappropriate in any way after we go to the market with it? Moreover, SVM was just an example of the classifier used; others like NN and linea ...
written 11 weeks ago by Floydian_slip130
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Is reusing a subset of features in another layer of classification wrong or over-fitting?
... Hi, I am using a machine learning code written by somebody else where they run the first level of classification using 10 features. Then they select some instances which were not classified with certainty (between a certain range of output value) and rerun them again with a smaller subset of those 1 ...
machine learning overfitting overtraining written 11 weeks ago by Floydian_slip130 • updated 11 weeks ago by Mensur Dlakic5.5k
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Confusing Picard HsMetrics ON_BAIT_VS_SELECTED for near=250 and near=0
... Hi, for an assay developed by my vendor, I ran latest Picard HsMetrics (2.21.8) with two different options for the same set of BAM files: one with a NEAR_DISTANCE=250 and one with NEAR_DISTANCE=0. The bait and Target interval file was the same. With the default value of NEAR_DISTANCE=250, I got ON_B ...
sequencing next-gen picard hsmetrics written 3 months ago by Floydian_slip130
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Comment: C: Calculate the area covered more than a certain depth
... More than the per base coverage, I am looking for the fraction of region in the bed file which is more than 100X to see how the experiment performed. Basically, I want to know how much fraction of the exome is covered with 100X or more. Do you know of a quick way to do that given the Bam file and th ...
written 7 months ago by Floydian_slip130
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Comment: C: Calculate the area covered more than a certain depth
... Hi yztxwd, this will give me the number of reads in each region. I am looking for number of bases in each region where the coverage is more than a certain depth (say 100X). Can I somehow replace the last 'samtools view' command above to count the bases above 100X? Thanks! ...
written 7 months ago by Floydian_slip130
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Calculate the area covered more than a certain depth
... Hi, I have an exome BAM file and a BED file of CCDS. How can I find out what fraction of my CCDS is covered at a depth higher than a threshold? Eg., I want to know what fraction of CCDS is above 100X. Thanks! ...
next-gen coverage bam sequencing written 7 months ago by Floydian_slip130 • updated 7 months ago by yztxwd380
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Dragen alignment failing/terminating
... Hi, I am running Dragen on my sample for alignment and it terminates/exits early without any error. I am new to the Dragen alignment world. I was wondering if there is anything in the .out file (copied below) which could hint if its a Dragen issue or a hardware issue? Can anybody advise me on what ...
alignment dragen written 8 months ago by Floydian_slip130
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Comment: C: List of conditions a set of genes are associated with in OMIM
... Thanks Corentin! It worked like a charm. ...
written 8 months ago by Floydian_slip130
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List of conditions a set of genes are associated with in OMIM
... Hi, I have a set of ~150 gene and I want to obtain a list of phenotypes (diseases or conditions) they are associated with. I was wondering what is the way to do this in OMIM in a batch manner. Eg., Gene Condition BRCA1 Breast Cancer Thanks for your help! ...
omim written 8 months ago by Floydian_slip130 • updated 8 months ago by Corentin450
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Comment: C: Bed file of union of all transcripts for a set of genes
... Example input: a list of genes such as BRCA1 and ALDH1. Desired output: a bed file containing their transcripts. I understand there will be multiple lines for each for each of the transcript regions. Thanks! ...
written 9 months ago by Floydian_slip130

Latest awards to Floydian_slip

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