User: Denis

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Denis190
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Posts by Denis

<prev • 99 results • page 1 of 10 • next >
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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 12 days ago by Denis190
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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 13 days ago by Denis190
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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 9 weeks ago by Denis190
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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 9 weeks ago by Denis190
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Comment: C: Prefetch error while downloading data from sequence read archive
... Thanks a lot. Will try different solutions. ...
written 9 weeks ago by Denis190
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Comment: C: Prefetch error while downloading data from sequence read archive
... Besides, i should to note that initially i have approximately 60 accessions and got error with `prefetch` only for 11 of them (everything were fine with the rest ones). Then i ran again exactly the same `prefetch` command for these 11 accessions and downloaded half of them (for 6 got error). ...
written 9 weeks ago by Denis190
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Comment: C: Prefetch error while downloading data from sequence read archive
... Thaks for your reply. I don't run them in parallel, but sequentially one by one inside one `for` loop. Before `prefetch` running i've executed: /home/sratoolkit.2.10.0-ubuntu64/bin/vdb-config -s /http/timeout/read=1000000000 It seems that above command helps but not in all cases. ...
written 9 weeks ago by Denis190
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Prefetch error while downloading data from sequence read archive
... Hi! I'm using `prefetch` command from `SRA Toolkit` on HPC cluster to download SRA data, but got stuck into error: 2020-03-26T16:34:59 prefetch.2.10.0 int: transfer incomplete while reading file within network system module - Cannot KStreamRead: https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2 ...
software error written 9 weeks ago by Denis190
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Comment: C: Aspera ascp command line utility inside prefetch call to facilitate SRA data dow
... Thanks a lot. Will try to manage that. ...
written 11 weeks ago by Denis190
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Comment: C: Aspera ascp command line utility inside prefetch call to facilitate SRA data dow
... Hi! That's interesting, as for me it takes almost 1 hour to download SRR6856357 with `prefetch` on HPC cluster. ...
written 11 weeks ago by Denis190

Latest awards to Denis

Centurion 12 days ago, created 100 posts.
Popular Question 7 weeks 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 8 weeks ago, created a question with more than 1,000 views. For Extract SNPs flanking sequences based on VCF and genome Fasta files
Popular Question 4 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 5 months ago, created a question with more than 1,000 views. For Extract SNPs from VCFfile located in genes based on GFF file information
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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 8 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 11 months ago, created an answer that has been accepted. For A: Bootstrap values on the phylogenetic tree in Ape r package
Teacher 11 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 12 months ago, created a question with more than 1,000 views. For Demultiplexing of the Illumina PE data
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