User: Begonia_pavonina

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Posts by Begonia_pavonina

<prev • 40 results • page 1 of 4 • next >
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Comment: C: merging overlaping ranges with GenomicRanges
... Thanks for these references. I have tried to use reduce(), but the result was not exactly what I was searching for. However, the range() function gave me the extremum of the chromosomes (Chr), and it was the one which provided the desired output. ...
written 16 days ago by Begonia_pavonina20
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Comment: C: merging overlaping ranges with GenomicRanges
... Thanks to have formalized my question in a proper way. ...
written 16 days ago by Begonia_pavonina20
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Comment: C: Keep metadata gc column using GenomicRanges
... Thank you very much for your answer benformatics. You have well understood my problem, and in my case the gc column is not numbers, so there is indeed no way to make a mean of it. ...
written 16 days ago by Begonia_pavonina20
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Comment: C: Replace FASTA file headers
... My apologizes, I thought the thumb up was the way to validate the answer. ...
written 16 days ago by Begonia_pavonina20
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Replace FASTA file headers
... Hello everyone, I try to replace the headers A of a FASTA file (file.fasta) with headers B. For this, I have a list which match the headers names. >A_1 >B_1 >A_2 >B_2 >A_3 >B_3 etc... I am using this loop to replace the headers: cat list | while ...
fasta loop sed written 16 days ago by Begonia_pavonina20 • updated 16 days ago by Joe18k
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Keep metadata gc column using GenomicRanges
... Hello everyone, I am using the GenomicRanges module in R to output the maximum and minimum of my genomic range object. First, the GRanges object has been designed with a file columns. Note that metadata have been added to the object using "gc=". > > gr <- GRanges(seqnames=file$V1, &g ...
iranges ranges R written 18 days ago by Begonia_pavonina20
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merging overlaping ranges with GenomicRanges
... Hello everyone, I have a BLASTN output file in the following format (-outfmt 6): > Chr1 contig_806 98.438 64 1 0 382055 382118 64 1 7.47e-23 113 > Chr1 contig_806 100.000 61 0 0 381772 381832 121 61 7.47e-23 113 > Chr1 contig_2215 95.367 259 11 1 262655 262913 267 10 2.36e-112 ...
R genomicranges blast range written 4 weeks ago by Begonia_pavonina20 • updated 4 weeks ago by Jeremy Leipzig19k
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Answer: A: How to build my resource-bundle for variant recalibrator?
... I have the same problem. A link for making custom training database was available here, but it seems broken now: https://evodify.com/gatk-in-non-model-organism/ I will try to get the link back and post it here. ...
written 5 weeks ago by Begonia_pavonina20
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Length of scaffolds in a FASTA file
... Hello everyone, A simple question, but I have not found a clear answer anywhere else. It seems very simple to do. I try to calculate the size of a genome scaffolds using simple bash commands. For example the first Scaffold: head -2 genome.faa | tail -1 | wc -c And whatever the row, characte ...
fasta genome scaffold bash written 7 weeks ago by Begonia_pavonina20 • updated 7 weeks ago by cpad011214k
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Comment: C: edit FASTA file according to range positions
... As I quote above, it is a very nice script for a single range replacement. If there is several replacement per Scaffold, then I think another tool should be used. Would anyone know what could be used in this specific case? ...
written 8 weeks ago by Begonia_pavonina20

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