User: Denis

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Denis200
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6 years, 8 months ago
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Posts by Denis

<prev • 104 results • page 1 of 11 • next >
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Comment: C: Merge overlapping and adjacent features in the BED file having the same label in
... Thanks for your quick reply! Just because i already have a `bedtools` installed on my PC, i've used solution suggested by Pierre Lindenbaum. ...
written 3 days ago by Denis200
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Comment: C: Merge overlapping and adjacent features in the BED file having the same label in
... I'm wondering which tool i can use to do that? ...
written 3 days ago by Denis200
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Merge overlapping and adjacent features in the BED file having the same label in the name (4-th) column
... Hi there! My `BED` file looks like: chr1 10 20 A chr1 15 20 B chr1 19 30 A chr1 10 20 C chr1 21 30 C I'd like to merge overlapping or adjacent (i.e. having just a 1bp distance) features with the same label in the `name` (the 4-th) column of the ...
genome R written 3 days ago by Denis200 • updated 3 days ago by Alex Reynolds31k
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Circos could not open image.conf error
... Hi, I'm performing some experiments with the `Circos` code from (just to learn `Circos`): [enter link description here][1] [1]: http://circos.ca/documentation/course/ But i got the error : *** CIRCOS ERROR *** cwd: /mnt/lustre/tkiy/Circos_test command: ../ ...
software error written 18 days ago by Denis200
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Running Mauve on circular genomes
... Hi! There are a batch of circular genomes i have to align with `Mauve`. The issue is that the genomes start at different positions. I'm wondering, if it's an important thing i should manage before the running of `Mauve` software ? I.e. should i somehow change the start coordinates in all the genome ...
genome alignment written 22 days ago by Denis200
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Comment: C: How to perform alignment of nucleotide sequence containing ambiguous bases
... Hi! I'm wondering how substitution from `W` to `R` will be treated in `nsm` matrix? Will it be a mismatch? ...
written 6 months ago by Denis200
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Comment: C: How to perform alignment of nucleotide sequence containing ambiguous bases
... Hi! I would not use `Disambiguate` if understand the output of this function correctly. With this approach you may generate a huge number of artificial sequences which does not exist even in nature not only in your samples. E.g. having a sequence `ARTY` does not mean that there are mandatory all of ...
written 6 months ago by Denis200
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Comment: C: Fast download of FASTQ files from the European Nucleotide Archive (ENA)
... Thank you again. Even if i used `wget` to download these? I have all the `*.fastq.gz` files in my output directory. ...
written 7 months ago by Denis200
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Comment: C: Fast download of FASTQ files from the European Nucleotide Archive (ENA)
... Thank you so much for the clarification! Unfortunately i downloaded several fastq files which for some reason i was not able to download via `prefetch` directly from ENA website. How i can verify completeness of these few `fastq` files? ...
written 7 months ago by Denis200
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Comment: C: Prefetch error while downloading data from sequence read archive
... Thanks a lot. Will try different solutions. ...
written 8 months ago by Denis200

Latest awards to Denis

Popular Question 4 months ago, created a question with more than 1,000 views. For Canonical Correspondence Analysis in R with Vegan library
Popular Question 4 months ago, created a question with more than 1,000 views. For Optimization of RNA-Seq data mapping with tophat2
Popular Question 4 months ago, created a question with more than 1,000 views. For Number of bases with a certain quality in FASTQ file
Popular Question 4 months ago, created a question with more than 1,000 views. For Convert blast tabular output to bed format
Popular Question 6 months ago, created a question with more than 1,000 views. For Canonical Correspondence Analysis in R with Vegan library
Centurion 6 months ago, created 100 posts.
Popular Question 7 months ago, created a question with more than 1,000 views. For Extract SNPs from VCFfile located in genes based on GFF file information
Popular Question 7 months ago, created a question with more than 1,000 views. For Extract SNPs flanking sequences based on VCF and genome Fasta files
Popular Question 10 months ago, created a question with more than 1,000 views. For Extract SNPs from VCFfile located in genes based on GFF file information
Popular Question 11 months ago, created a question with more than 1,000 views. For Extract SNPs from VCFfile located in genes based on GFF file information
Voter 11 months ago, voted more than 100 times.
Popular Question 13 months ago, created a question with more than 1,000 views. For Extract SNPs from VCFfile located in genes based on GFF file information
Popular Question 14 months ago, created a question with more than 1,000 views. For Extract SNPs from VCFfile located in genes based on GFF file information
Scholar 17 months ago, created an answer that has been accepted. For A: Bootstrap values on the phylogenetic tree in Ape r package
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Bootstrap values on the phylogenetic tree in Ape r package
Popular Question 18 months ago, created a question with more than 1,000 views. For Demultiplexing of the Illumina PE data
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