User: ando.kelli

gravatar for ando.kelli
ando.kelli40
Reputation:
40
Status:
New User
Location:
University of Tasmania
Website:
http://www.utas.edu.au...
Scholar ID:
Google Scholar Page
Last seen:
1 month, 1 week ago
Joined:
6 years, 10 months ago
Email:
a*********@gmail.com

Hey all,

I'm currently working as an academic at the University of Tasmania. 

My background and publications can be viewed at the pages below.

https://au.linkedin.com/in/kelli-anderson-a5014631

http://scholar.google.com.au/citations?user=d9f1Z2MAAAAJ&hl=en

Kel

Posts by ando.kelli

<prev • 27 results • page 1 of 3 • next >
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Comment: C: Customise blastn to exclude key words
... Yep for sure Genomax. I'm talking about transcripts that have been annotated using Blastn with quite stringent parameters, but the annotation not informative. I want to improve the existing annotation if possible. I'm happy to filter out transcripts that don't have high quality hits. ...
written 6 weeks ago by ando.kelli40
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Comment: C: Customise blastn to exclude key words
... Thanks Genomax. If I can't annotate them I can't use them, so for me filtering them is the equivalent of deleting them. ...
written 6 weeks ago by ando.kelli40
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Comment: C: Customise blastn to exclude key words
... Thanks for your input genomax and Mansur Dlakic. Filtering the offending hits out of the database isn't what I want to do, because that's the same as deleting them from my dataset. I'd rather annotate them if possible because many of them are differentially expressed. ...
written 6 weeks ago by ando.kelli40
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Customise blastn to exclude key words
... Hi All, I'm annotating a transcriptome against NCBI's nt database, and was wondering if I could get some advice regarding customisation. A lot of the hits are to genomes: e.g. 'Salmo trutta genome assembly, chromosome: 13' which doesn't tell me anything about what the transcript might be. (I'm d ...
ncbi blast blastn linux written 6 weeks ago by ando.kelli40 • updated 6 weeks ago by genomax80k
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Comment: C: Indexing error with local blast
... Thanks again Genomax :-) ...
written 12 weeks ago by ando.kelli40
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Comment: C: Indexing error with local blast
... Hi again Genomax, I split my assembly so that I can do the annotation in parallel. When I run the following code, the output is missing sscinames sskingdom ls trinity_out_dir.Trinity.*.fasta | parallel --eta -j 10 --load 80% --noswap 'blastn -db /volume/BlastDBs/nt -query {} -out blastn_outfi ...
written 12 weeks ago by ando.kelli40 • updated 12 weeks ago by genomax80k
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Comment: C: Indexing error with local blast
... Wow. I can't believe that's what the issue was. Thank you so much Genomax!! ...
written 12 weeks ago by ando.kelli40
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Indexing error with local blast
... Hi all, I'm trying to do a blast to local NCBI nt database in Linux. The code I've used to download and decompress the DB is: cd /volume/BlastDBs update_blastdb.pl nt update_blastdb.pl taxdb gunzip *tar.g* ls *.tar |xargs -n1 tar -xvf Notes: I needed to do a lo ...
annotation database blast rna-seq linux written 12 weeks ago by ando.kelli40 • updated 12 weeks ago by genomax80k
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Comment: C: Problem with Trinity's abundance_estimates_to_matrix.pl
... The --out_prefix flag doesn't exist anymore for the latest release when using align_and_estimate_abundance.pl which is the one that creates the input files for abundance_estimates_to_matrix.pl. Instead, it creates individual sub-directories for each sample that include the sample name in the direct ...
written 2.2 years ago by ando.kelli40
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Answer: A: Problem with Trinity's abundance_estimates_to_matrix.pl
... In the latest version of Trinity, the program works on directories that are named as opposed to the output files like in v2.4.0. The abundance_estimates_to_matrix.pl script uses the isoform estimates to compute the gene level estimates based on the gene-trans-map info. This is also different compa ...
written 2.2 years ago by ando.kelli40

Latest awards to ando.kelli

Popular Question 18 months ago, created a question with more than 1,000 views. For TMM.normalized.FPKM vs .TMM.EXPR.matrix for populating SQL
Popular Question 23 months ago, created a question with more than 1,000 views. For TMM.normalized.FPKM vs .TMM.EXPR.matrix for populating SQL
Popular Question 23 months ago, created a question with more than 1,000 views. For Combine multiple fasta files in galaxy?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Combine multiple fasta files in galaxy?
Supporter 3.3 years ago, voted at least 25 times.
Autobiographer 3.5 years ago, has more than 80 characters in the information field of the user's profile.

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