User: Dracaena

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Dracaena30
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30
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New User
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Last seen:
10 months ago
Joined:
1 year, 4 months ago
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Posts by Dracaena

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Choosing the right BLAST result when using multiple databases
... Thanks for the fast reply! I appreciate it. I have used the command line blast. So these value I have are out of this blast. Now I blasted the sequence in the browser using NCBI. The results for *A. thaliana* turn up the same as. The result for *A. chinensis* however are totally different with no go ...
written 10 months ago by Dracaena30
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Choosing the right BLAST result when using multiple databases
... Hi guys, I am a little bit stuck in choosing the right blast result. I have a protein sequence of a non model organism I am interested in (*Primula veris*, plant). I have successfully performed a blast for this protein against 2 databases, 1 being *A. thaliana* (one of the best reviewed and most re ...
proteinblast blast written 10 months ago by Dracaena30
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Comment: C: BLAST Database error: No alias or index file found for protein database
... This solved it for me! Thanks, altough I don't understand why some people have the opposite problem, i.e. that it does not work withouth adding .fasta. ...
written 10 months ago by Dracaena30
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BLAST Database error: No alias or index file found for protein database
... Hi guys, I just downloaded a protein fasta file for Arabidopsis which I want to blast my data to. What I did is, I have put the fasta file in a folder, I have used the "makeblastdb" command: Building a new DB, current time: 11/28/2018 11:21:43 New DB name: /mnt/d/Primula/Databases/Athali ...
database blast error written 10 months ago by Dracaena30 • updated 10 months ago by Joe14k
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Answer: A: Picard Tools runs out of space when running Poolparty pipeline
... Ok guys, I just tried adding the TMP_DIR in the config file and it worked. Picard Tools used that DIR as temp. Poolparty does not mention that this is possible, but apparantly it is. Nice! ...
written 11 months ago by Dracaena30
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Picard Tools runs out of space when running Poolparty pipeline
... Hi all, I am using a pipeline to align and analyze NGS data called "Poolparty" ( https://github.com/StevenMicheletti/poolparty ). Overall it's a great way to do so since it delivers both VCF and sync (popoolation) files. The only problem is, that I don't have enough space in my /tmp directory and t ...
ngs next-gen picard tools poolparty out of space written 11 months ago by Dracaena30
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Comment: C: Fetch gene names from SNP coordinates
... Sorry, I confused it with SAMtools. ...
written 12 months ago by Dracaena30
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Comment: A: Fetch gene names from SNP coordinates
... Some clarification, my SNPs file looks something like this: 1 15 1 516 1 468 3 156 4 468 7 456 7 753 So it gives the scaffold number on which the SNP is located (I am working with a draft genome) together with the base number in that scaffold where the SNP is. Al ...
written 12 months ago by Dracaena30
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Fetch gene names from SNP coordinates
... Hi all, Currently I have positions of SNPs in the format of "contig position" e.g. "2 1564". I also have an annotation file in gff format that goes along with the draft genome I am working with. Now I want to retrieve the ID of each gene that has a SNP in it. I know BEDtools does this, but it requi ...
genome annotation snp gene written 12 months ago by Dracaena30 • updated 12 months ago by mike-zx140
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Comment: C: Are scaffolds in published draft genomes always ordered?
... Thank you for your answer! ...
written 14 months ago by Dracaena30

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