User: gtasource

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gtasource20
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Posts by gtasource

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Comment: C: Optimize AUGUSTUS Segmentation Fault
... Unfortunately no, besides the: Segmentation fault (core dumped) Could not read the accuracy values out of predictions.txt when processing bucket 1. at /home/Aug/scripts/optimize_augustus.pl line 1224. And then also a failed to execute braker.pl error. ...
written 9 days ago by gtasource20
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Comment: C: Optimize AUGUSTUS Segmentation Fault
... I have the CPU average chart in front of me. I started BRAKER2 around 10PM last night, and CPU usage hovered around 97%. Right before the Optimize Augustus step (that keeps failing) it went down to 80%. Here's the full command that keeps failing: perl /home/Aug/scripts/optimize_augustus.pl - ...
written 9 days ago by gtasource20 • updated 9 days ago by genomax59k
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Optimize AUGUSTUS Segmentation Fault
... Not sure if anybody will be able to help, but I've been using the BRAKER2 pipeline and everything has been running fine, up until I reach the optimize AUGUSTUS step. Here's how it's failing: Segmentation fault (core dumped) Segmentation fault (core dumped) Segmentation fault (core dump ...
augustus braker written 9 days ago by gtasource20
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Coordinates for Gene in Unannotated Reference FASTA
... I have a species with an unannotated reference FASTA. I have gene coordinates that I pulled from NCBI from very closely related annotated species (each gene is 10,000 - 30,000BP long.) I want to map these genes to the unannoated reference FASTA so that I can have have coordinates for this new speci ...
annotation blast blat written 8 weeks ago by gtasource20
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DE Gene List to Regulatory Network
... Hi all, Just finished a DE gene pipeline, and now I have a list of candidate genes. I'm looking to construct some regulatory networks. Any tutorials, or information on how to begin would be great! ...
R de edger gene regulatory network written 9 weeks ago by gtasource20
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Comment: C: Only One Blast Result Per Query (Lowest E-Value)
... Question. I recently read this article: https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/bty833/5106166?redirectedFrom=fulltext Does max_target give the lowest e-value? Or just any result that matches reaches the threshold. ...
written 10 weeks ago by gtasource20
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Only One Blast Result Per Query (Lowest E-Value)
... I'm BLASTING to get gene names, and am only interested in the lowest E-value BLAST result for each query. From there, I'm looking to extract the gene name. How can this be done? I'm using the online server version of BLAST, but can easily transition to Linux. ...
blast written 10 weeks ago by gtasource20
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BLAT Results to BED for each Gene
... Hi guys, I have the results from my BLAT search, where I used BLAT to search a list of genes against a reference fasta. I now have a huge list of results and coordinates for each gene against this reference. What I want to do now is to take the best match (or the longest) for each of these genes, ...
blat written 10 weeks ago by gtasource20
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FASTA to Gene Names (Is BLAST the best option)
... Dealing with an unannotated genome. I have the sequences of genes I'm interested in knowing the names of (in fasta format.) The idea was to simply BLAST them against a species that we believe is closely related. However, is there any other options or software that might be best suited? ...
blast written 11 weeks ago by gtasource20 • updated 11 weeks ago by Biostar ♦♦ 20
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Too Many StringTie Genes
... I'm using Stringtie on aligned RNA-seq data, for a species without a GTF file. Problem is, Stringtie is just predicting way too many genes (~100K.) What kind of things can I do to become more stringent and reduce the amount of genes that are being predicted? Thanks! ...
stringtie written 11 weeks ago by gtasource20

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