User: hed.robin

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hed.robin20
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Posts by hed.robin

<prev • 9 results • page 1 of 1 • next >
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Bacterial mobile elements database
... Hello! I've been looking for a database of known bacterial mobile elements excluding (pro)phages: plasmids, transposons and IS's. And I couldn't find any. ISfinder's database is only available on web. I want to detect known bacterial transposons and IS's in metagenomic samples. Does anyone know if ...
transposons metagenome is written 19 days ago by hed.robin20
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Command line tool for Helix-Turn-Helix motif predictions
... Is there a command line tool for helix-turn-helix motif prediction that accepts protein fasta? I can see online tools only... ...
motif prediction written 12 months ago by hed.robin20 • updated 12 months ago by genomax49k
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Comment: C: How do you people tell if a gene is really present in the sample after mapping t
... yep it's a situation that can happen on the edge of a sequence, if you have quite a short sequence and long reads, so you allow local mapping. I've solved my problem with filtering by coverage breadth and average coverage depth per base. ...
written 18 months ago by hed.robin20
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How to remove adapters from DNA-seq illumina reads?
... Hi all, I have some metagenomics reads, I trim them with trimmomatic and remove adapters using some illumina adapters library I found on the internet. Then I look at them in Fastqc and it says that "adapter content" is very bad and "kmer content" is very bad as well (which must mean that there are ...
trimming sequencing written 18 months ago by hed.robin20 • updated 18 months ago by Macspider2.4k
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Comment: C: How do you people tell if a gene is really present in the sample after mapping t
... Well lets say I got some bit numbers in terms of reads count, and then I realize that they are mapping not just a part of a gene, but a very very small portion of a gene that is even less than a read. So I am wondering, is there any common way to count all of this, like, in one formula? Or I have t ...
written 19 months ago by hed.robin20
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Comment: C: How do you people tell if a gene is really present in the sample after mapping t
... Thank you for the answer and for the link explaining the RPKM, but I'm afraid I wasn't clear enough on that I have the DNA reads, so I'm trying to determine physical presence of a gene as a DNA sequence. ...
written 19 months ago by hed.robin20
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Comment: C: How do you people tell if a gene is really present in the sample after mapping t
... No, it is not RNAseq, it is DNA, so I guess it is sorta like lights off and on. ...
written 19 months ago by hed.robin20
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How do you people tell if a gene is really present in the sample after mapping the reads on the gene?
... I have a set of gene sequences. And some sets of reads. I mapped these reads on the genes that I have and now I'm wondering about the best way to tell whether a gene is really present in the samples that I'm analyzing. We use read_count /(gene_length*number_of_reads_in_sample) formula to compa ...
gene bowtie sequencing written 19 months ago by hed.robin20 • updated 19 months ago by Macspider2.4k
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Answer: A: A few words for R beginners
... Russian-speaking R beginners should definitely take R courses on stepik.org, they are good and some tasks are difficult and that's good for your brain ...
written 21 months ago by hed.robin20

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Popular Question 19 days ago, created a question with more than 1,000 views. For How to remove adapters from DNA-seq illumina reads?

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