User: Floydian_slip

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Floydian_slip130
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Posts by Floydian_slip

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Answer: A: average depth of each region in a BED file calculated from a BAM file
... I ended up using "samtools bedcov" and then writing a quick script to divide the total base pairs (last column) by the length of the region. I matched that up with Samtools depth and it matches. Thanks for your help, RamRS! ...
written 25 days ago by Floydian_slip130
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Comment: C: average depth of each region in a BED file calculated from a BAM file
... Thanks, RamRS. I was able to install it using docker but ran into error: $docker run -v ~/Documents/ quay.io/biocontainers/mosdepth:0.2.4--he527e40_0 mosdepth -n --fast-mode -b ~/Documents/redesign_sorted.bed ~/Documents/sample ~/Documents/ecs-ready.bam [E::hts_open_format] Failed to open ...
written 4 weeks ago by Floydian_slip130 • updated 4 weeks ago by RamRS30k
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Comment: C: average depth of each region in a BED file calculated from a BAM file
... Thanks for the reply, RamRS! Running into installation issues with mosdepth. Any way either samtools or bedtools can do this for me? ...
written 4 weeks ago by Floydian_slip130
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average depth of each region in a BED file calculated from a BAM file
... Hi, I have a list of regions in a BED file and I want to know the *average* depth of each region as calculated from a BAM file, ideally as the fourth column in the output file (like an extra column in the BED file). Is there some combination of Samtools/Bedtools and awk that I can use to get this? T ...
bed ngs bam coverage written 4 weeks ago by Floydian_slip130
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Comment: C: Quickly get allele frequencies from Gnomad
... Thanks! this is perfect! ...
written 4 weeks ago by Floydian_slip130
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Quickly get allele frequencies from Gnomad
... Hi, I would like to know the AF of ~4000 rsIDs (dbSNP) quickly in Gnomad GRCh37 database. I looked at the instructions for getting this from Gnomad and it seems I would need to download the entire data. Is there is a faster and less involved way fo getting the AF from Gnomad without downloading more ...
allele freq ngs gnomad written 5 weeks ago by Floydian_slip130
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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 6 months 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 6 months ago by Floydian_slip130 • updated 6 months ago by Mensur Dlakic6.4k
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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 7 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 11 months ago by Floydian_slip130

Latest awards to Floydian_slip

Great Question 6 months ago, created a question with more than 5,000 views. For difference between BWA mem, sampe and bwasw
Great Question 6 months ago, created a question with more than 5,000 views. For demultiplexing tool for dual-indexed paired-end illumina libraries
Popular Question 6 months ago, created a question with more than 1,000 views. For high depth Illumina samples from 1000 Genomes
Popular Question 2.7 years ago, created a question with more than 1,000 views. For extracting genotypes from a multi-sample VCF that have certain variants
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Mapability index from UCSC
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Individual or population level variant calling?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For number of .bam reads mapping to genes in gff format
Popular Question 2.7 years ago, created a question with more than 1,000 views. For cuffmerge does not give merged.gtf
Popular Question 2.7 years ago, created a question with more than 1,000 views. For difference between BWA mem, sampe and bwasw
Student 2.7 years ago, asked a question with at least 3 up-votes. For demultiplexing tool for dual-indexed paired-end illumina libraries
Student 2.7 years ago, asked a question with at least 3 up-votes. For demultiplexing Illumina output with fastq_multx
Popular Question 2.8 years ago, created a question with more than 1,000 views. For picard tools HsMetrics not using duplicate reads to calculate coverage
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Individual or population level variant calling?
Popular Question 4.2 years ago, created a question with more than 1,000 views. For number of .bam reads mapping to genes in gff format
Popular Question 4.2 years ago, created a question with more than 1,000 views. For cuffmerge does not give merged.gtf
Popular Question 4.2 years ago, created a question with more than 1,000 views. For difference between BWA mem, sampe and bwasw
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Picard MarkDuplicates error: Value was put into PairInfoMap more than once
Popular Question 4.2 years ago, created a question with more than 1,000 views. For importance of known sites/resources in GATK pipeline
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Known SNPs for rice for Base recalibration using GATK
Popular Question 4.3 years ago, created a question with more than 1,000 views. For cuffmerge does not give merged.gtf
Popular Question 4.5 years ago, created a question with more than 1,000 views. For cuffmerge does not give merged.gtf

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