User: Dracaena

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Dracaena30
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2 months, 4 weeks ago
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9 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 3 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 3 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 3 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 3 months ago by Dracaena30 • updated 3 months ago by jrj.healey11k
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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 4 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 4 months ago by Dracaena30
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Comment: C: Fetch gene names from SNP coordinates
... Sorry, I confused it with SAMtools. ...
written 5 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 5 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 5 months ago by Dracaena30 • updated 5 months ago by mike-zx130
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Comment: C: Are scaffolds in published draft genomes always ordered?
... Thank you for your answer! ...
written 7 months ago by Dracaena30

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