User: alex.zaccaron

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Posts by alex.zaccaron

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Answer: C: Fasta extraction from bed file
... Sounds like you want to extract the sequences in the correct orientation and your 3-column bed file has reversed coordinates if sequence is in the reverse strand. Modifying ATpoint suggestion, you could still use bedtools getfasta to extract the correct orientation with: awk 'OFS="\t" {if($2> ...
written 5 days ago by alex.zaccaron30
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Comment: C: Polish PacBio assembly with Hi-C reads
... Thanks h.mon for the suggestion. Like you pointed out, using only end-to-end mapped reads could still be useful to polish regions of the genome. I will give it a shot and see how it looks. ...
written 6 days ago by alex.zaccaron30
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Polish PacBio assembly with Hi-C reads
... Hello, I have a small haploid genome (85 Mb) that was assembled with Canu based on ~100x of PacBio Sequel reads. In addition, a batch of 40 Gbp Hi-C Illumina reads was sequenced to perform scaffolding. The assembly has been polished with Arrow, but there is not a third dataset of Illumina reads to ...
assembly sequencing written 6 days ago by alex.zaccaron30
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Comment: C: "count"in the snpEFF html output
... As far as I know, the number of MODIFIER SNPs reported by SnpEFF does not reflect the number of distinct SNPs classified as MODIFIER. I haven't found in its manual, but I believe SnpEFF count them per gene, which may cause it to count them more than once. For example, if a SNP is downstream of gene ...
written 9 months ago by alex.zaccaron30
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Comment: A: Trimmomatic not trimming the adapter
... You could try a different tool e.g. [fastp][1]. [1]: https://github.com/OpenGene/fastp ...
written 9 months ago by alex.zaccaron30
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Answer: A: Popoolation variance-sliding.pl output shows only zero value
... Looks like Popoolation finds no SNPs within the sliding windows. That would explain why it is not calculating the measures. You could really have no SNPs in those regions, or there are SNPs but Popoolation is not considering them due to failing the filtering steps e.g. minimum quality. Keep in mind ...
written 9 months ago by alex.zaccaron30 • updated 9 months ago by genomax70k

Latest awards to alex.zaccaron

Scholar 5 days ago, created an answer that has been accepted. For C: Fasta extraction from bed file
Teacher 5 days ago, created an answer with at least 3 up-votes. For C: Fasta extraction from bed file

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