User: Elizabeth

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Elizabeth20
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2 years, 5 months ago
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Posts by Elizabeth

<prev • 27 results • page 1 of 3 • next >
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Mapping reads to reference genome + Denovo assembly
... Dear all, I am trying to assemble Illumina miseq reads (2x300bp) for my eukaryotic organism. I have the reference genome of an organism of a related species and I would like to use it for my assembly process. I have finished all the basic steps after I received my fastq files such as FTM, adapter re ...
reads reference genome blocks denovo assembly written 16 months ago by Elizabeth20
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Comment: C: removing adapters from illumina miseq paired end output files
... Thank you. bbduk.sh works. The adapters have been removed and I performed some quality filtering on the adapter trimmed reads as well to ensure uniform length distribution. Thanks again ...
written 17 months ago by Elizabeth20
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Comment: C: removing adapters from illumina miseq paired end output files
... This leads me to another question, do the paired-end reads be concatenated before trimming ? ...
written 17 months ago by Elizabeth20
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Comment: C: removing adapters from illumina miseq paired end output files
... I tried using both the reads as well, but the adapters are still present. I will try bbduk. Thanks. ...
written 17 months ago by Elizabeth20
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removing adapters from illumina miseq paired end output files
... Dear all, I am working on assembling the genome of a eukaryotic organism (smaller genome size ~65 Mb). As the first step, I performed a QC on the raw reads file (fastq files recieved after a Miseq 2x 300 run). In the results, I saw that the reads have adapters in the 3' end, also some of the reads ...
adapter removal illumina miseq written 17 months ago by Elizabeth20 • updated 17 months ago by genomax89k
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Comment: C: Command for counting gene model after each round of MAKER
... Thank you. It works. ...
written 17 months ago by Elizabeth20
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Command for counting gene model after each round of MAKER
... Hello, I am looking for a command that can tell me the number of gene models after each round of MAKER. I have tried the following: less Maker2.all.gff |awk '$3=="mRNA"' |grep "mRNA-1" |awk '{print $5-$4}' |summary.sh cat | awk '{ if ($3 == "gene") print $0 }' | awk '{ sum += ($5 - $4 ...
count gene model maker written 17 months ago by Elizabeth20 • updated 17 months ago by ringourquia20
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Comment: C: Alienness HGT results
... I apologize. HGT : Horizontal Gene Transfer Alienness http://alienness.sophia.inra.fr/cgi/index.cgi CEGMA http://korflab.ucdavis.edu/datasets/cegma/ BUSCO https://busco.ezlab.org/ ...
written 20 months ago by Elizabeth20
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Alienness HGT results
... Hello everyone. I recently ran Alienness to scan for HGT candidates in our eukaryotic protein sequence set (around 11500 proteins). The results section has a file titled 'possible contamination' and there are about 5000 proteins in it. This doesn't make sense. We ran BUSCO on our genome and predict ...
hgt alienness written 20 months ago by Elizabeth20
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Comment: C: Negative Log likelihood value for gene tree using MEGA
... Yes it does help a bit. Based on that link, I gather that it is commonplace to have negative log likelihood values for phylogenetic trees? ...
written 24 months ago by Elizabeth20

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