User: nattzy94

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nattzy9410
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Posts by nattzy94

<prev • 29 results • page 1 of 3 • next >
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Normalizing DNA sequencing reads using DNA spike in [sanity check]
... My main goal is to quantify absolute abundance of a known bacterial sample. My samples have either E. coli, K. pneumoniae or both. These are lab-grown cultures so I know which samples have which bacteria. In order to calculate absolute abundance, I spiked-in a known amount of a 150bp fragment of th ...
sequencing written 11 days ago by nattzy9410
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Comment: C: Having trouble using wildcard
... Yes, the original command had a typo but I've corrected it and the file still cannot be found. I've edited the initial post to reflect this. ...
written 3 months ago by nattzy9410
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Comment: C: Having trouble using wildcard
... I get './temp_expt/Sample_MBM118/MBM118-TTACGTGC-CAAGGTCT_S66_L008_R1_001.fastq' NB: I realize the previous command is missing a '1' and should be MBM1${i} but the problem still persists. ...
written 3 months ago by nattzy9410
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Having trouble using wildcard
... I am trying to use the bbsplit function for a number of files. I have done: for i in {17..34}; do bash bbmap/bbsplit.sh \ in1=./temp_expt/Sample_MBM1${i}/MBM1${i}_R1_001.fastq \ in2=./temp_expt/Sample_MBM1${i}/MBM1${i}_R2_001.fastq \ ref=./MG1655.fasta,./MGH78578.fast ...
command line loop shell written 3 months ago by nattzy9410 • updated 3 months ago by Michael Dondrup46k
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Comment: C: How to Align to multiple reference genomes -> Discard multiply mapped reads?
... Hey h.mon, Thanks for the suggestion. I have used BBsplit to generate the fastq files that mapped to the corresponding genomes. Just to check, in order to get the number of mapped reads, do I just convert the .fastq files to .bam files and use samtools? ...
written 3 months ago by nattzy9410
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How to Align to multiple reference genomes -> Discard multiply mapped reads?
... Hi, I have reads containing E. coli, K. pneumoniae and GAPDH spike-in. I would like to align these reads to the 3 genomes and then discard reads that map to more than one of the references. So far, I have concatenated all 3 fasta files into 1 composite genome. I have then used `bwa mem -c 1 ` ...
alignment bwa cmd written 3 months ago by nattzy9410 • updated 3 months ago by h.mon25k
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How to run Bracken on windows?
... Hi, I have been tasked with calculating the relative abundance of bacterial reads in a samples containing 2 different bacteria genomes. My supervisor has suggested using Bracken but I cannot seem to download it on to my windows computer? The manual says to use sh install_bracken.sh to install but ...
sequencing written 5 months ago by nattzy9410
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Comment: C: How do I use Glimmer 3.02?
... Ok, thanks for the help so far. Will take a look at the tutorial. I am trying to replicate methods for gene prediction and functional annotation in this paper: http://aem.asm.org/content/82/24/7063.full ...
written 15 months ago by nattzy9410
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Comment: C: How do I use Glimmer 3.02?
... Yes, I get a whole bunch of unix executable files in the 'bin' folder. However, when I open them, all I get is a terminal window in which I can't type anything. screenshot of the terminal window after opening Glimmer: https://ibb.co/hLsbSx ...
written 15 months ago by nattzy9410
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Comment: C: How do I use Glimmer 3.02?
... I downloaded Glimmer from https://ccb.jhu.edu/software/glimmer/ onto my mac and followed the installation instructions. Is that correct? ...
written 15 months ago by nattzy9410

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Popular Question 3 months ago, created a question with more than 1,000 views. For How do I use Glimmer 3.02?

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