User: gtasource

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gtasource20
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Posts by gtasource

<prev • 44 results • page 1 of 5 • next >
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Differential Expression of Single Gene
... Hi all, I have 6 aligned BAM files for a species I am working with. We have a single gene we want to see if it's differential. I'd rather not have to run an entire DE analysis when we just want to see if one specific gene is differential. My plan was to extract the gene coordinates and run BedTo ...
gene expression de-seq expression written 4 months ago by gtasource20 • updated 4 months ago by geek_y9.7k
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Parsing RepeatMasker Output Files
... Hi all, I put a FASTA file that had roughly 65,000 different scaffolds into RepeatMasker. I want to parse the output file to do the following: 1.) Tell me the total length of a certain type of repeat throughout the entire FASTA. 2.) Tell me the length, percentage, and times of appearance of a cer ...
fasta repeatmasker written 5 months ago by gtasource20
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GMAP or Bowtie index from FASTA of genes
... Hi all, I'm looking to use either Bowtie2 or GMAP/GSNAP to try to map sequences to gene names. The FASTA file that I want to index contains all of the genes from a species. Problem is, I keep getting errors when I try to index this FASTA file, as GMAP wants a chromosomal assembly I believe. The ...
gmap bowtie written 5 months ago by gtasource20 • updated 3 months ago by Biostar ♦♦ 20
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Mapping Gene Models Back to a Reference Genome of Closely Related Species
... I have about ~50,000 gene models from an unannotated species, that I am looking to map back to a reference genome of a closely related one. The issue I keep running into when I am BLASTing the gene models to the reference genome is that multiple gene models are going to the same gene. I want to use ...
gmap bowtie written 5 months ago by gtasource20 • updated 5 months ago by Vitis2.1k
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Comment: C: how to collecting all isoforms of a gene from Trinity.fasta file ?
... Sorry to bring an older post back up, but I've been trying to use this script and it doesn't seem to be outputting anything for me. Any help would be appreciated! ...
written 6 months ago by gtasource20
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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 6 months 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 6 months ago by gtasource20 • updated 6 months ago by genomax68k
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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 6 months 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 7 months 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 8 months ago by gtasource20

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