User: magnuskerber

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Posts by magnuskerber

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Comment: C: Read length for metagenomics analysis
... Thank you all, your answers are helping me a lot. Yes, I will trimm my data always prior to analysis. I got the whole idea about the over-represented sequences, they're not necessarily a bad thing. My library was generated using the TruSeq kit from Illumina. I got the adapter sequences from their we ...
written 5 weeks ago by magnuskerber0
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Comment: C: Read length for metagenomics analysis
... Ok, thank you Mensur. I'll make a 70bp cut then. My data has a good quality so that is a good thing. I have a question about the overrepresented sequences removal, in my case they are around 50bp ( I know that by making a 70bp cut they'll be removed, but I'm asking for curiosity/knowledge). Here is ...
written 5 weeks ago by magnuskerber0
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Comment: C: Read length for metagenomics analysis
... Thanks h.mon, those are the images. So, I think I'll use a cutoff of 50bp. Is that ok based on the graphics? Or can I go a little bit higher, like 70-90? ...
written 6 weeks ago by magnuskerber0
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Comment: C: Read length for metagenomics analysis
... >Did you remove over-represented sequences as idenfied by FastQC? Why? You should remove adapters and other contaminants, but not necessarily over-represented sequences: these may represent the more abundant organism in your dataset, not contamination of any kind. That is interesting, do you us ...
written 6 weeks ago by magnuskerber0 • updated 6 weeks ago by h.mon27k
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Comment: C: Read length for metagenomics analysis
... **Do you consider useful a read of 1 nucleotide in length?** Hahah, of course no. About the highly conserved region the data is not only 16s, I'm not sure if you referred to that. **So you may perform a histogram of the read length distribution and take a decision based on that.** So, this is inter ...
written 6 weeks ago by magnuskerber0 • updated 6 weeks ago by h.mon27k
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Comment: C: Read length for metagenomics analysis
... Yes, I thought about that. The thing is I didn't find any defined number for read size, I will use MEGAHIT for assembling. Do you use 25bp in a regular basis? ...
written 6 weeks ago by magnuskerber0
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Read length for metagenomics analysis
... Hi guys! So, I am an undergraduate student in bioinformatics and I am starting to perform and study metagenomics/microbiome analysis. I have some data generated through Illumina Hi-Seq. My reads vary between 1-151bp. So, below I will explain shortly what I've done by now: - I cleaned my data, by ...
gene assembly reads metagenomic written 6 weeks ago by magnuskerber0 • updated 6 weeks ago by Buffo1.7k

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