User: kieft1bp

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kieft1bp0
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Posts by kieft1bp

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Comment: C: What exactly does the -fs flag (fragment size) do in bedtools genomecov/genomeCo
... Thanks for your simple answer. So, in my case from above, if I have a read that is 50 bp long it will be *trimmed* to 20 bp, and if I have a read that is 10bp it will be *extended* to 20bp in order to calculate final per-bp coverage? ...
written 7 weeks ago by kieft1bp0
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What exactly does the -fs flag (fragment size) do in bedtools genomecov/genomeCoverageBed?
... I am trying to extract per-base read mapping coverage from a BAM file based on several regions of interest in a BED file. For example, I want to get the coverage at each base pair for the following 1kb regions: chr start end name score strand chrI 182604 183604 region1 0 - chrII 197700 ...
bedtools bed bam read mapping written 7 weeks ago by kieft1bp0 • updated 7 weeks ago by ATpoint44k
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Comment: C: How can I calculate the C:N ratio (or just number of carbons and nitrogens) of e
... Yes, you're right. I was just wondering if there was a tool already that was written to solve the same task. Just trying not to reinvent the wheel. ...
written 24 months ago by kieft1bp0
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Comment: C: How can I calculate the C:N ratio (or just number of carbons and nitrogens) of e
... Thanks for the answer, Pierre, but the problem is a little more complicated than counting the instances of a string in each line. I've updated my question. My fasta sequences are just amino acids (with no information about carbon or nitrogen content), so what I actually need to do is reference a sep ...
written 24 months ago by kieft1bp0
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How can I calculate the C:N ratio (or just number of carbons and nitrogens) of each amino acid sequence in a multifasta file?
... I have a multifasta file of amino acid sequences, around 1000 seqs total, like so: - > seq_id_1 - MAWT........ - > seq_id_2 - MTRA....... - .... - > seq_id_1000 - MIVE....... I want to calculate the molar C:N ratio (number of total carbon atoms in each sequence divided by the n ...
protein carbon nitrogen statistics written 24 months ago by kieft1bp0

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