User: allerdrengen55

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Posts by allerdrengen55

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Comment: C: Mapping to contigs or predicted genes, for quantitative gene analysis (DNAseq)
... So there is no universal way to normalize my genes? My samples could potentially differ pretty much in terms of abundance of genes (levels?), so those tools won't be able to help? ...
written 1 day ago by allerdrengen5520
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Comment: C: Tool to extract COG information/description
... I just realized, that some COGs have multiple letters. Is that because the gene harbors both categories or because it doesn't know where to put it? ...
written 1 day ago by allerdrengen5520
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Comment: C: Mapping to contigs or predicted genes, for quantitative gene analysis (DNAseq)
... Hi Asaf, thanks for your response! A couple of questions: Is count matrix referring to the contig alignment? How would you suggest I normalize my genes? (Longer genes, will have more mapped reads than shorter genes) ...
written 1 day ago by allerdrengen5520
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Comment: C: Mapping to contigs or predicted genes, for quantitative gene analysis (DNAseq)
... That is noted, thanks! ...
written 1 day ago by allerdrengen5520
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Mapping to contigs or predicted genes, for quantitative gene analysis (DNAseq)
... Hi! A little background: I have a metagenomic sample (DNA-seq). I want to figure out the gene depth/abundance of all the genes in the sample. Since there a lot of different (and same) bacteria in the sample, I expect some of the genes to have a high abundance. Keep in mind that it is a DNA-seq, so ...
dnaseq fastq alignment contigs map written 1 day ago by allerdrengen5520 • updated 1 day ago by Asaf6.4k
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Answer: A: Using featureCount with a GFF file
... I found the issue. I was using an alignment of the genes rather than the chromosomes, hence the confusion. I made a new alignment, and everything looks good now! ...
written 1 day ago by allerdrengen5520
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Comment: C: Using featureCount with a GFF file
... So I have to alter one of the files, so they match (Either to 003__g__Streptococcus_no_23 or PLMABFGE_05378)? 003__g__Streptococcus_no_23 is a contig name, and since multiple genes have been annotated from that contig, multiple IDs (PLMABFGE_05378 for instance) have been generated. So how can I make ...
written 2 days ago by allerdrengen5520
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Comment: C: Using featureCount with a GFF file
... Hi Michael, Thanks for your response. I see. One question though: How can my alignment be on transcriptome level, when I'm dealing with DNA data? And how can the alignment differ from the gff? The alignment is made with paired-end FASTQ files mapped to the ffn-files outputted from Prokka (the same ...
written 2 days ago by allerdrengen5520
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Comment: C: Tool to extract COG information/description
... Hi Mensur! That's exactly what I was looking for. I suppose a small script could easily fetch the right COGs from it. The A-Z letters are a very general categorization, right? ...
written 3 days ago by allerdrengen5520
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Tool to extract COG information/description
... I have list of different COG numbers, and would like to retrieve a list of the COG numbers, with their corresponding function. Is there a tool for this?¨ The COG numbers look like this (always 4 digits): COG:COG1132 ...
cog written 3 days ago by allerdrengen5520

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Scholar 1 day ago, created an answer that has been accepted. For A: Using featureCount with a GFF file

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