User: Bea

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Bea0
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Posts by Bea

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How to transfer gff3 annotation from scaffolds to reference genome?
... Good afternoon everyone, I am doing genome skimming to retrieve microsatellite loci from my genomic dataset. To start, I filtered the raw Illumina reads (2x150bp) with Trimmomatic and then did an assembly de novo with SPAdes. Then, I mapped the SPAdes scaffolds to the reference nuclear genome for ...
annotation genome skimming microsatellite written 5 weeks ago by Bea0
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Comment: C: Low percentage of Illumina reads retained after trimming with Trimmomatic
... Thank you. Regarding your reasoning about the coverage, I thought the same, but then I was told that many reads won't belong to the chloroplast genome (they may as well be from the nuclear genome), so that calculation is in the ideal situation where all reads are actually coming from the chloroplast ...
written 5 months ago by Bea0
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Comment: C: Low percentage of Illumina reads retained after trimming with Trimmomatic
... Thanks, I'll try to use BBDuk for comparison with Trimmomatic and map the trimmed reads between 30 and 130 to the cultivated species chloroplast genome to check if I can pool something out of those. If I get anything good I'll give an update. ...
written 5 months ago by Bea0
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Comment: C: Low percentage of Illumina reads retained after trimming with Trimmomatic
... Thank you for the replies! JV: I did not do the labwork, but what I know is that the quality and fragmentation of the DNA (extracted with cTAB) were checked with a Quantus machine and via electrophoresis in agar gel. The quality and fragmentation of the libraries were checked again with a Quantus m ...
written 5 months ago by Bea0 • updated 5 months ago by ATpoint16k
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Low percentage of Illumina reads retained after trimming with Trimmomatic
... Good morning everyone, This is my first question in Biostars, so please bear with me if it is not well structured. I am currently processing raw Illumina paired end reads to proceed with the assembly of 96 chloroplast genomes. Whole genome shotgun libraries were prepared using the NEBNext Ultra I ...
genome trimmomatic sequencing written 5 months ago by Bea0 • updated 5 months ago by ATpoint16k

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