User: Antonio R. Franco
Antonio R. Franco • 4.5k
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Posts by Antonio R. Franco
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Comment:
C: K-mer analysis meaning
... you need to investigate the using of the de Bruijn graph to explain this.
Certainly, the assembling of genomes using kmers can at least in some cases have certain adventages over the assembling done using the overlapping method ...
written 2 days ago by
Antonio R. Franco • 4.5k
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... We have assembled HiFi PacBio reads with an haploid-aware assembler (hifiasm). It is a tree genome
After analyzing the over 7900 contigs we got (expected genome size of 1,8Gb), we got these results obtained after using BUSCO, where it can be seen a very high number of duplicated sequences
![BUSCO a ...
written 3 days ago by
Antonio R. Franco • 4.5k
• updated
3 days ago by
lieven.sterck ♦ 9.4k
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... I would say the first is plural and the second singular
They are the same concept ...
written 8 days ago by
Antonio R. Franco • 4.5k
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... Of course. Give it a try ...
written 9 days ago by
Antonio R. Franco • 4.5k
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... Look into KEGG by prior selection of your organism
If you have the protein sequences and cann't find the KO codes, look for [BlastKoala][1] which is a tool included into KEGG to annotate them
[1]: https://www.kegg.jp/blastkoala/ ...
written 9 days ago by
Antonio R. Franco • 4.5k
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... One cluster gives you a read. The genome is attained after using an assemble program ...
written 20 days ago by
Antonio R. Franco • 4.5k
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... Any odd flag has the byte 1 on because paired end reads were used in the mapping
Obviously any even flag number means you were mapping single reads
...
written 20 days ago by
Antonio R. Franco • 4.5k
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... If you have already your Illumina reads, and try to map to the reference genome, you need an splice aware mapper such as HISAT2 or STAR to unravel the junctions. You are comparing reads coming from mature RNA without introns with a reference genome that have them. ...
written 29 days ago by
Antonio R. Franco • 4.5k
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... This would not be told a year ago...
I would go to run IsoSeq sequencing with PacBio HiFi to answer this question
Why?
1. Prices for PacBio sequencing has dropped dramatically. If can be pretty similar to that of Illumina nowdays
2. IsoSeq sequencing involves the true sequencing of your RNA popu ...
written 29 days ago by
Antonio R. Franco • 4.5k
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... The problem here is how interpret these differences. I understand from your table that your RNA-Seq indicates that there is not expression of your genes, whereas the qPCR indicates that this not true.
What of these two pieces of information shall we trust?
In my opinion, RNA-Seq contains a trusted ...
written 11 weeks ago by
Antonio R. Franco • 4.5k
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For A: How to find the Genes present in the sequence?
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For A: Must know algorithms before attending a bioinformatics interview
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