User: alex.zaccaron

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alex.zaccaron200
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Posts by alex.zaccaron

<prev • 35 results • page 1 of 4 • next >
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Comment: C: Convert .sqn file to .gbk
... You can try [NCBI sequin][1]. You should be able to load your .sqn file with the `Read existing record` option, and then `File > Export GenBank`. [1]: https://www.ncbi.nlm.nih.gov/projects/Sequin/download/seq_download.html ...
written 8 days ago by alex.zaccaron200
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Comment: C: How to check for completeness of a mitochondrial or chloroplast genome?
... I am not aware of a dataset to estimate completeness of organelle genomes, but mitochondrial genomes should have a somewhat standard set of genes. Plus, they usually do not have a lot of genes, you could annotate your contigs and check the genes manually. ...
written 11 days ago by alex.zaccaron200
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Comment: C: mummer dot plot
... Hi rthapa. No, it shouldn't matter for mummer to call SNPs and INDELs if the two genomes have different start points. ...
written 12 days ago by alex.zaccaron200
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Comment: C: Pac bio assembler
... You could provide some details of what you are trying to assemble. There are discussion about it already. Check [here][1], and a (not that recent) review paper [here][2]. But [Canu][3] is among the top assemblers out there. [1]: https://www.biostars.org/p/330613/ [2]: https://www.nature.com/ar ...
written 5 weeks ago by alex.zaccaron200
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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 8 months ago by alex.zaccaron200
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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 9 months ago by alex.zaccaron200
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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 9 months ago by alex.zaccaron200
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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 9 months ago by alex.zaccaron200
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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 9 months ago by alex.zaccaron200
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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 9 months ago by alex.zaccaron200

Latest awards to alex.zaccaron

Scholar 8 months ago, created an answer that has been accepted. For C: Fasta extraction from bed file
Scholar 17 months ago, created an answer that has been accepted. For C: Fasta extraction from bed file
Teacher 17 months ago, created an answer with at least 3 up-votes. For C: Fasta extraction from bed file
Scholar 18 months ago, created an answer that has been accepted. For C: Fasta extraction from bed file
Teacher 18 months ago, created an answer with at least 3 up-votes. For C: Fasta extraction from bed file

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