User: jblommaert92

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jblommaert9270
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Posts by jblommaert92

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Comment: C: MAKER command maker2zff .ann and .dna files are empty
... I'll add that I tried both maker2zff with and without the -n option, both produced empty files and no error ...
written 17 months ago by jblommaert9270
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Comment: A: MAKER command maker2zff .ann and .dna files are empty
... Hi, I'm having the same issue and I'd like to know if anyone has found a solution to this? My MAKER run went well, and the gff3_merge command worked well, but then when I call maker2zff, it produces and empty .ann and an empty .dna file ...
written 17 months ago by jblommaert9270
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Comment: C: NCBI TaxIds from Diamond Blast output
... This worked perfectly, and I almost understand it too, thanks! ...
written 2.9 years ago by jblommaert9270
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Comment: C: NCBI TaxIds from Diamond Blast output
... I'm not sure exactly how EUtils works, and the example uses accession numbers, not versions. Using my blast output and the bash script from the other question only gave me a blank output, so I thought the problem might be accession numbers? I also just tried entering http://eutils.ncbi.nlm.nih.gov/ ...
written 2.9 years ago by jblommaert9270
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NCBI TaxIds from Diamond Blast output
... Hi, This question will seem INCREDIBLY similar to the question [here][1], but it's not. I ran diamond blastx on a large dataset with the output options -f 6 qseqid sseqid bitscore This gives me a file that looks like OHJ07_1_contig_1 ELU09376.1 66.6 OHJ07_1_contig_1 KFM76682.1 65.9 O ...
genome ncbi taxid blast written 2.9 years ago by jblommaert9270 • updated 2.9 years ago by Petr Ponomarenko2.6k
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Answer: A: Oxford Nanopore and Illumina hybrid assembly
... Just thought I'd add the few options I've seen: 1) OPERA-LG https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0951-y 2) PacBio reccomendations may be relevant here https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Large-Genome-Assembly-with-PacBio-Long-Reads 3) ...
written 3.0 years ago by jblommaert9270
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Comment: C: Bash- Sort a file based on a list in another file
... Sorry for the delayed response, I tried this method and it works well, thanks! (Biostars told me I was posting too much and I couldn't reply anymore) ...
written 3.0 years ago by jblommaert9270
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Comment: C: Bash- Sort a file based on a list in another file
... Yeah, but since I have contig name and length already in a file, I'm still not sure why the first processing of file1 is necessary? ...
written 3.0 years ago by jblommaert9270
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Comment: C: Bash- Sort a file based on a list in another file
... Sorry, I forgot to mention that file2 has contig length in column 2, is there any reason why can't I use this? Is it because there is only one row per contig in file2 and file1 has multiple rows per contig? ...
written 3.0 years ago by jblommaert9270
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Comment: C: Bash- Sort a file based on a list in another file
... Why do I need the first step if the second step sorts file1 based on my list of contigs anyway? ...
written 3.0 years ago by jblommaert9270

Latest awards to jblommaert92

Popular Question 21 months ago, created a question with more than 1,000 views. For Bash- Sort a file based on a list in another file
Popular Question 21 months ago, created a question with more than 1,000 views. For NCBI TaxIds from Diamond Blast output
Appreciated 21 months ago, created a post with more than 5 votes. For A: Oxford Nanopore and Illumina hybrid assembly
Student 2.8 years ago, asked a question with at least 3 up-votes. For NCBI TaxIds from Diamond Blast output
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Oxford Nanopore and Illumina hybrid assembly

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