User: euduca

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euduca0
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Posts by euduca

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How to determine the c-terminal and n-terminal regions of a proteome of a non-model organism?
... Hello everyone, I have come for some time looking for some way to determine (using bioinformatics) the c-terminal and n-terminal regions of a non-model organisms (in this case a plant). The proteome has more than 30,000 proteins. I read some questions here in the group, but nothing that could help ...
c-terminal n-terminal proteins interproscan written 8 months ago by euduca0 • updated 8 months ago by Michael Dondrup44k
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Comment: C: Is NCBI closing down due to lack of funding?
... No problems. Fourteen years ago once my boss asked me how much space it would take if we wanted to copy everything. According to him, if the US entered into some kind of conflict the access would be lost. So when I saw this warning on NCBI's website, the question he asked me over ten years ago came ...
written 9 months ago by euduca0
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(Closed) Is NCBI closing down due to lack of funding?
... ![enter image description here][1] [1]: http://i.imgur.com/AQ2ZO9o.jpg Is the NCBI is closing down due to lack of funding? We know when the governments wants to cut their spending, research is always a good point to start. And I have one more question: how much disk space do I need to make ...
blast written 9 months ago by euduca0 • updated 9 months ago by Santosh Anand4.0k
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Comment: C: DISOPRED3 Blastpgp Failed 256
... Hi Yamule. You're right about the variable $SEQ_DB. I fixed this. But the error still persisted, so I figured out that variable $BLASTDB was pointed, by default, to the NR database in the HPC. So, before to run the script I set the variable $BLASTDB to: export BLASTDB=/scratch/eac16/dbs/blas ...
written 12 months ago by euduca0
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DISOPRED3 Blastpgp Failed 256
... Hi, all =) I'm trying to use de DISOPRED3 program, but this error appears: $ ../run_disopred.pl ../examples/example.fasta Running PSI-BLAST search ... [../run_disopred.pl] ERROR: /home/eac16/local/ncbi/blast/legacy/2.2.26/bin/blastpgp -i /home/eac16/local/DISOPRED/3.16/examples/ ...
blastpgp disopred3 failed 256 legacy blast written 12 months ago by euduca0
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Answer: A: "Optimal" setting of CPU and max_memory in Trinity
... See this: http://trinityrnaseq.github.io/performance/mem.html See the options "--bflyCalculateCPU", "--bflyCPU", "--bflyHeapSpaceMax", "--normalize_reads" (quality trimming and the in silico normalization are currently not compatible), and "--max_memory. ...
written 18 months ago by euduca0
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Comment: C: Can I design a Circos image without an existent genome reference?
... Hi. Thanks for the answer. The three biotypes are from the same species, so I chose to study a group of genes that are related to virulence factors (effectors) and regions with low similarity ( I want to discover the differences bettween among the biotypes) is interesting too. That's what I hav ...
written 21 months ago by euduca0
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Can I design a Circos image without an existent genome reference?
... Hi, I have three de novo assemblies (with predicted genes and their annotations) of three differents biotypes from a same specie of fungus. There is no reference genome, so I don't know how many chromossomes exists. I found some assemblies from related species, but there is no mention to chromossome ...
assembly circos written 21 months ago by euduca0 • updated 21 months ago by mforde841.2k
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Merging illumina paired-end data Lxxx and R1/R2
... Hi. I received paired-end illumina data for some DNA sequencing (Hiseq). There are four fastq files and are named like this: Fungal_L001_R1_001.fastq and Fungal_L001_R2_001.fastq Fungal_L002_R1_001.fastq and Fungal_L002_R2_001.fastq They are from the same library (TruSeq LT DNA kit, insert size o ...
open paired-end next-gen merge sequencing written 2.8 years ago by euduca0 • updated 2.8 years ago by Dan Gaston7.1k

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Popular Question 17 months ago, created a question with more than 1,000 views. For Merging illumina paired-end data Lxxx and R1/R2

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