User: lamteva.vera

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lamteva.vera10
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Ukraine, Kyiv
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1 day, 22 hours ago
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Posts by lamteva.vera

<prev • 21 results • page 1 of 3 • next >
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Comment: C: From FASTQ to clean BAM using GATK tutorial #6484
... GATK claims that > Broadly, the tool [MergeBamAlignment] merges defined information from the unmapped BAM > (uBAM, step 1) with that of the aligned BAM (step 3) to conserve read > data, e.g. original read information and base quality scores. ...
written 4 days ago by lamteva.vera10
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From FASTQ to clean BAM using GATK tutorial #6484
... Hi! I'm trying to build an efficient pipeline for processing amplicon sequencing data. The problem is that ValidateSamFile reveals a bunch of errors in BAM files after running BamClipper (whereas BAMs were free of errors before). Exemplary output of ValidateSamFile (MODE=SUMMARY): HISTOGRAM j ...
gatk forum bamclipper ubam mergebamalignment written 4 days ago by lamteva.vera10
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Comment: C: Different BAM files generated using different commands in bash - which one is ri
... Yes, I've read this, thank you. I got it. I'm going to call variants - OK, let BAMs look different in IGV if variant calls are going to be the same... I just want to know if I can use the aformentioned for loop to process FASTQ files in pairs, and different sized BAMs make me worry. ...
written 10 days ago by lamteva.vera10
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Comment: C: Different BAM files generated using different commands in bash - which one is ri
... But, you know, they still look different in IGV: ![enter image description here][1] [1]: https://i.imgur.com/FOKAMD8.png I need to use a more accurate way to compare them. Right now trying to find out the way... ...
written 10 days ago by lamteva.vera10
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Comment: C: Different BAM files generated using different commands in bash - which one is ri
... Thank you for your comment. I tried without `sudo`: for f in `ls /media/sf_Desktop/170303_M04607_0037_000000000-AR7YC/*fq | rev | cut -c 22- | rev | sort -u` do bwa mem -t 2 ucsc_hg19.fasta -R "@RG\tID:${f}\tSM:${f}\tPL:ILLUMINA\tLB:${f}" ${f}_L001_R1_001.clean.fq ${f}_L001_R2_001.clea ...
written 10 days ago by lamteva.vera10
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Different BAM files generated using different commands in bash - which one is right?
... Dear friends, please help me to understand what I am doing wrong. I'm doing my best to figure out how to use Linux for the purposes of NGS analysis. Now I am trying to use a for loop to iterate over fastq files named like this: LK_S2**_L001_R1_001.clean.fq** (constant part is bold). To test it, I ...
bam bash written 10 days ago by lamteva.vera10
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Comment: C: How long does it take to build a pipeline?
... Thank you for your time! Thanks for pointing me to Environmental Modules, I'll try to figure out how this works. I suppose my systems administrator could help with logging. I have a naive question: what are the built-in controls and how to use them? ...
written 13 days ago by lamteva.vera10
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Forum: How long does it take to build a pipeline?
... Hi to everyone, thanks for your kind support. I am a biologist (geneticist more specifically) working at the molecular diagnostics lab, who was tasked with building a bioinformatics pipeline for Illumina's TrueSeq Custom Amplicon panel designed to be used as a preconception carrier screening analys ...
self-learning next-gen forum written 13 days ago by lamteva.vera10 • updated 13 days ago by 5heikki6.7k
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Comment: C: Which command line programs are parallelizable?
... Dear Brian, when running bbduk, it is restricted to only one pair of fastq.gz files, how can it be overcome? ...
written 13 days ago by lamteva.vera10
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Comment: C: Sequence length distribution after adapter trimming
... Thank you, genomax. What are the factors to consider when setting the threshold for `minlen` or `mlf`? ...
written 18 days ago by lamteva.vera10

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