User: jnowacki

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jnowacki70
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Posts by jnowacki

<prev • 29 results • page 1 of 3 • next >
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Comment: C: Base count NOT read count - Downsampling to specific number of bases not reads?
... This seems to work. Thank you! The number seem to line up extremely well when confirmed with this method: - awk 'BEGIN{sum=0;}{if(NR%4==2){sum+=length($0);}}END{print sum;}' file.fq And off by more than 1% when confirmed with this method: - cat test.fastq | paste - - - - | cut -f 2 | tr -d ' ...
written 11 months ago by jnowacki70
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Comment: C: Base count NOT read count - Downsampling to specific number of bases not reads?
... I just want to guarantee 13x coverage. I'm comparing the performance of multiple wet lab protocols. The following variables changed between samples: - Reference: (hg19, hg38, etc) - Bed file: - multiple capture technologies - Read length - Wet lab protocols The project was designed by a ...
written 12 months ago by jnowacki70
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Base count NOT read count - Downsampling to specific number of bases not reads?
... How to I down-sample to say 13 million bases total? **Quick summary:** I'm trying to get even depth of coverage and each fastq file has different read lengths & reference size. **More details:** I have 60 samples and each fastq file has slightly different read length. So down-sampling by re ...
reads bases fastq downsample seqtk written 12 months ago by jnowacki70 • updated 12 months ago by genomax91k
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Comment: C: GC Bias in Sequence Capture - Analysis & Quantification
... I'm trying to detect GC bias. The problem with the normal HsMetrics output is not all of the bed regions are the same size so any binning/graphing will heavily weight the results towards whatever GC content is contained in average of the smaller regions. ...
written 19 months ago by jnowacki70
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GC Bias in Sequence Capture - Analysis & Quantification
... **QUESTION** I have a bed file & alignment file (bam). I'd like to know if the reads contained inside the bam are biased towards GC rich regions. **RESEARCH** Picard CollectGcBiasMetrics does a great job with whole genome sequencing but doesn't take bed files as input. Picard HsMetrics can te ...
bed sequence capture picard gcbias sequencing written 19 months ago by jnowacki70 • updated 18 months ago by Biostar ♦♦ 20
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(Closed) Punching a hole in firewall -- to install cutadapt via pip (What ports, ip, protocol, address?)
... I'm trying to request our very security conscious IT team to open up ports so I can get to cutadapt. I need to know port, protocol & IP address. Any help? I found this link https://stackoverflow.com/questions/22377175/what-ports-does-pip-use which says Port - 3128 Port - 443 (confl ...
firewall security pip written 2.4 years ago by jnowacki70
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Depth of Coverage - Calculated Per Probe / Bed Region
... I'm trying to find out the average depth of coverage per target region in a bed file. I can easily use bedtools -depth to find the depth of coverage at each base, but I'd much rather have it as average coverage per region. The bedtools "-hist" option produces 110 reports on one of my features. ...
bed bam tool depth written 2.8 years ago by jnowacki70 • updated 2.8 years ago by Kevin Blighe66k
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Comment: C: Tool For Counting Adapter Dimer: I need metrics NOT trimming
... but does it report dimers? I'm not concerned with adapters. I'm concerned with adapter dimers that have not library sequence. Thank you for the response. ...
written 3.2 years ago by jnowacki70
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Tool For Counting Adapter Dimer: I need metrics NOT trimming
... Any tools out there that give adapter dimer metrics? I don't care if they trim or don't trim I just need adapter dimer counts to see how messy our wetlab protocol is. ...
adapter dimer adapters trimming dna primer dimer written 3.2 years ago by jnowacki70 • updated 3.2 years ago by chen2.1k
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Metagenomic Mappers & Benchmark Datasets?
... I'm looking to map a mixture of bacteria to known references and classify their abundance. What are the top tools for this? Q1) Top tools for meta-genomics mapping Q2) Control data-sets I can use to verify my metagenomic mapping pipeline? I am familiar with assembly data-sets and tools. For inst ...
metagenomics mapping written 3.3 years ago by jnowacki70 • updated 3.3 years ago by Samuel Brady320

Latest awards to jnowacki

Popular Question 19 months ago, created a question with more than 1,000 views. For How does Bowtie2 handle chimeric singletons?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For VCF Files: Help on 0/1 1/1 0/0 1/1 | vs / (phased & unphased
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Depth of Coverage - Calculated Per Probe / Bed Region

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