User: venura

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venura10
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3 days ago
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1 month, 3 weeks ago
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v*****@agri.pdn.ac.lk

Posts by venura

<prev • 19 results • page 1 of 2 • next >
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Comment: C: Error : viGEN : bowtie2 Alignment - No input read files were valid
... Thank you! I screwed up the samplenames.txt where I added underscore. :( ...
written 18 days ago by venura10
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Error : viGEN : bowtie2 Alignment - No input read files were valid
... Hi, I am using [viGEN][1] pipeline to identify viruses in RNA-Seq data. I am getting following error when I run the script. > stat: No such file or directory Warning: Could not open read file "/home/venura/viGEN-master/unmapped_fastq/RRV4_un/RRV4_un__1.fq" for reading; skipping... Error: No i ...
bowtie2 allignnment rna-seq written 19 days ago by venura10
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Comment: C: MCScanx is giving an Empty Output (even for example files)
... Please see the below answer. That approach worked for me. I am no code expert so there might be much simpler approaches. ...
written 24 days ago by venura10
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Comment: A: MCScanx is giving an Empty Output (even for example files)
... Preparing files for BLAST - I downloaded the protein fasta file from Ensembl plants - I used the following command to remove unnecessary info sed -r '/>/ s/.*\gene:(.*)transcript:.*/>\1/' test.fa (convert >PGSC0003DMT400092485 pep chromosome:SolTub_3.0:3:15516123:15519502:-1 gene:P ...
written 24 days ago by venura10
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Answer: A: MCScanx is giving an Empty Output (even for example files)
... I found the solution thanks to a good folk at reddit. > Solution is to put .blast and .gff file inside MCScanX folder without creating a separate folder. Big thank goes to threesup @reddit. ...
written 25 days ago by venura10
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Comment: C: MCScanX result problem
... Did you find a way ? ...
written 29 days ago by venura10
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MCScanx is giving an Empty Output (even for example files)
... Hi, I am getting following error from MCScanx. I initially thought it has to do something with the input files I am used. I have MCScanx properly setup after incorporating `" #include " msa.h, dissect_multiple_alignment.h, and detect_collinear_tandem_arrays.h` . I am using Linux Mint. > ## ...
mcscanx mcscan written 29 days ago by venura10
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Comment: C: Error: legacy_blast.pl command not found
... Hello venura! We believe that this post does not fit the main topic of this site. found a solution. For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree please tell us why in a reply below, we'll b ...
written 4 weeks ago by venura10
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Comment: C: Error: legacy_blast.pl command not found
... Thank you! I know its not possible. But, I am darn sure that blast was there in the $PATH earlier :(. ...
written 4 weeks ago by venura10
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Comment: C: Error: legacy_blast.pl command not found
... When I use the full path as you suggested, I get the help file. When I echo, i get the following `#path/home/venura/miniconda3/bin:/home/venura/miniconda3/condabin:/home/venura/bin:/home/venura/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games` ...
written 4 weeks ago by venura10

Latest awards to venura

Scholar 25 days ago, created an answer that has been accepted. For A: MCScanx is giving an Empty Output (even for example files)

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