User: alex.zaccaron

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alex.zaccaron170
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Posts by alex.zaccaron

<prev • 31 results • page 1 of 4 • next >
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Answer: C: Analysis of host-parasite mixed transcriptome
... In my case, I mapped the RNA-seq reads to both host and parasite genomes simultaneously, after concatenating their genomes. Then, I removed unmapped reads and reads with primary alignment to the host chromosomes (I was interested in the parasite). From my point of view, if you remove reads that map ...
written 18 days ago by alex.zaccaron170
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Comment: C: Why the Trimmomatic does not remove some adapters? How do I add a new sequence t
... If you can afford use a different tool, try [fastp][1], which can auto detect the adaptor sequence and is much faster than Trimmomatic. BBduk from [BBMap][2] is also a good one, which comes with a comprehensive list of adaptors (`adapters.fa`). [1]: https://github.com/OpenGene/fastp [2]: https ...
written 4 weeks ago by alex.zaccaron170
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Comment: C: Error downloading streams from SRA-ncbi when running fastq-dump
... Instead of using `fastq-dump` you could try [sra-explorer][1] and get the links to download the fastq files. [1]: https://sra-explorer.info ...
written 4 weeks ago by alex.zaccaron170
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Comment: C: Correct gtf file format (AGAT toolkit)
... `AGAT` should produce a correct GTF file. Is there anything wrong with your GFF? A new version of `AGAT` was released recently and a few issues were fixed. Try to update it. ...
written 4 weeks ago by alex.zaccaron170
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Comment: C: Too many unmapped reads - STAR alignment
... Try to map with a different tool to see if you get different results. Since you're mapping to a transcriptome, you could try BWA. ...
written 5 weeks ago by alex.zaccaron170
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Comment: C: Gene prediction programs predicting different genes
... Sounds like your initial prediction (Augustus) is in better accordance with homologs in other species, and therefore more likely to be correct. Regarding the two genes predicted by Funannotate, you actually would see the same PFAM domain in both; imagine that the conserved domain was "broken" into t ...
written 6 weeks ago by alex.zaccaron170
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Answer: C: Gene prediction programs predicting different genes
... Gene prediction is not perfect, mis-annotated genes are quite common. Because fungi usually have very compact genomes, predicted genes that are merged (two genes called as one) or split (one gene called as two) usually occour. It is always a good idea for non-model organisms to manually curate genes ...
written 6 weeks ago by alex.zaccaron170
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Answer: A: TransDecoder in Linux
... Looks like you are trying to predict ORFs within assembled transcripts (that is what TransDecoder does). If you successfully ran `TransDecoder.LongOrfs -t target_transcripts.fasta`, then TransDecoder produces a few files, including `longest_orfs.pep` which already has the amino acid sequences of the ...
written 8 weeks ago by alex.zaccaron170
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Comment: C: How can I fix frameshift errors in assembled genome?
... You can use Quiver (if you have old RS reads) or Arrow (Sequel reads) to polish your assembly. You can also give Pilon a try. The newest version supports long reads. ...
written 3 months ago by alex.zaccaron170
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Comment: C: Contig longer than mitochondrial sequence. Explanation ?
... If you expect a circular mitochondrial genome, it is possible that the ends of the assembled contig overlap, which makes it longer than the expected. You can check it fairly quick by aligning the contig to itself (e.g. with [Gepard][1]). [1]: http://cube.univie.ac.at/gepard ...
written 4 months ago by alex.zaccaron170

Latest awards to alex.zaccaron

Scholar 17 days ago, created an answer that has been accepted. For C: Fasta extraction from bed file
Scholar 9 months ago, created an answer that has been accepted. For C: Fasta extraction from bed file
Teacher 9 months ago, created an answer with at least 3 up-votes. For C: Fasta extraction from bed file
Scholar 10 months ago, created an answer that has been accepted. For C: Fasta extraction from bed file
Teacher 10 months ago, created an answer with at least 3 up-votes. For C: Fasta extraction from bed file

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