User: Dracaena
Dracaena • 30
- Reputation:
- 30
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- New User
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- Last seen:
- 2 months, 4 weeks ago
- Joined:
- 9 months ago
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Posts by Dracaena
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... 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
Dracaena • 30
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... 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 ...
written 3 months ago by
Dracaena • 30
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... 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
Dracaena • 30
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... 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 ...
written 3 months ago by
Dracaena • 30
• updated
3 months ago by
jrj.healey ♦ 11k
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... 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
Dracaena • 30
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... 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 ...
written 4 months ago by
Dracaena • 30
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... Sorry, I confused it with SAMtools. ...
written 5 months ago by
Dracaena • 30
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... 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
Dracaena • 30
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... 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 ...
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... Thank you for your answer! ...
written 7 months ago by
Dracaena • 30
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