User: Pryce Michener

Reputation:
10
Status:
New User
Location:
Memphis, TN
Last seen:
2 years, 8 months ago
Joined:
4 years, 5 months ago
Email:
p************@gmail.com

Posts by Pryce Michener

<prev • 10 results • page 1 of 1 • next >
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Velvetg not producing output files
... I am running VelvetOptimiser, and the code works through velveth and velvetg, but velvetg does not produce any of the output files that its supposed to. I don't have the stats.txt file in the output directories, meaning that VelvetOptimiser won't continue. My log files are below, does anyone have an ...
velvetg velvet written 2.7 years ago by Pryce Michener10 • updated 2.7 years ago by k.kathirvel93200
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VelvetOptimiser getting an unknown option error
... I'm trying to run VelvetOptimiser, and I keep getting the following error: >VelvetOptimiser.pl Version 2.2.5 >Number of CPUs available: 32 >Current free RAM: 122.174GB >Velvet OMP compiler setting: 1 >Unknown option: fasta -shortpaired pairedreads_paired.fasta -fasta -short sin ...
assembly velvet written 2.9 years ago by Pryce Michener10
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How to use de novo assembly to build onto an existing reference-guided assembly.
... I recently used the published carrot mitochondrial genome as a reference to assemble draft mitochondrial genomes for 28 of the species that I study from raw Illumina HiSeq reads. The results came out really well, but I'm getting a lot of gaps in the assemblies. I was wondering what the best way woul ...
de novo assembly written 3.6 years ago by Pryce Michener10 • updated 3.6 years ago by h.mon27k
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Comment: C: How to filter short length blast results from output
... This gives me a different error: Traceback (most recent call last):   File "XML_filter2.py", line 5, in <module>     blast_records=NCBIXML.read(result)   File "/apps/python/2.7.6/lib/python2.7/site-packages/Bio/Blast/NCBIXML.py", line 542, in read     raise ValueError("More than one record f ...
written 3.9 years ago by Pryce Michener10
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Comment: C: How to filter short length blast results from output
... Thank you for this script! I'm having a few problems with it, however. I'm getting the following error: Traceback (most recent call last): File "XML_filter2.py", line 6, in <module> for alignment in blast_records.alignments: AttributeError: 'generator' object has no attribute 'alignmen ...
written 3.9 years ago by Pryce Michener10
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How to filter short length blast results from output
... I'm currently trying to work with a set of plant nucleotide contigs that are all greater than 300 bp in length. I'm trying to use NCBI blast to identify the contigs, but I'm running into a problem because my outputs tend to be flooded with ~50 bp long sequences in my contigs that match with random d ...
blast written 3.9 years ago by Pryce Michener10 • updated 3.9 years ago by Siva1.6k
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Comment: C: Mauve aligner without SML files
... Hey, I realize this was a long time ago, but I'm having the same problem and keep running into roadblocks. How did you solve it? ...
written 4.0 years ago by Pryce Michener10
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Generating a phylogeny from 5 different species' nuclear de novo assemblies
... I have 5 nuclear de novos and I was attempting to build a phylogeny out of them, but I'm running into a brick wall. I was initially trying to use MrBayes, but I can't figure out how to format the nexus file. My .fasta files are set up like this: >scaffold3 Locus_16_0 16.4 COMPLEX GAGTTTGCAAGGAA ...
phylogeny assembly written 4.1 years ago by Pryce Michener10 • updated 4.1 years ago by h.mon27k
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Comment: C: Detecting transposable elements in both assembled genomes and raw reads
... Thanks for the answer, I wasn't aware that that RepeatModeler worked this way. I want to compare TEs between sister species and sister clades, so I guess that RepeatModeler might not be the best choice here. Do you know anything about REPCLASS?  I will look at Transposome. I really appreciate the h ...
written 4.1 years ago by Pryce Michener10
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Detecting transposable elements in both assembled genomes and raw reads
... I'm trying to detect and identify transposable elements in my plant genomes, and I'm having some trouble finding the best programs and pipelines to use. The major reviews of these programs all seem to have come out 5-8 years ago, and I wasn't able to find anything that covered newer programs since t ...
transposable elements transposons tes written 4.1 years ago by Pryce Michener10 • updated 4.1 years ago by SES8.2k

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