User: Santiago Montero-Mendieta

Reputation:
120
Status:
Trusted
Location:
Sweden
Website:
http://santiagomontero...
Twitter:
biomendi
Scholar ID:
Google Scholar Page
Last seen:
4 days, 20 hours ago
Joined:
2 years, 10 months ago
Email:
b*******@gmail.com

I am a PhD student at the Conservation and Evolutionary Genomics Group at Estación Biológica de Doñana (CSIC), Seville, Spain. In summertime Spain is really hot, so I go to work at Biomedicinskt centrum (BMC), Uppsala, Sweden. I'm interested in speciation processes, conservation resources, and genomic divergences. To learn more about me, please visit my website.

 

Posts by Santiago Montero-Mendieta

<prev • 27 results • page 1 of 3 • next >
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Answer: A: How I can change many names of list file
... Assuming that you want to modify the content of a .txt file, you can achieve that in many different ways, for example with sed: sed -i -e 's/.adjust//g' your_file.txt ...
written 13 months ago by Santiago Montero-Mendieta120
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Comment: C: How to identify single-copy genes across multiple complete genomes?
... Cool, so I will have to filter the Orthogroups (= gene families) and keep single-copy genes only. Seems that someone already did a program for that: https://github.com/davidemms/OrthoFinder/issues/72. But how to match the sequences extracted with HybPiper to the list of single-copy genes? I guess us ...
written 13 months ago by Santiago Montero-Mendieta120
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How to identify single-copy genes across multiple complete genomes?
... A month ago, I asked a question on how to detect paralog sequences in target enrichment when single-copy genes are NOT known: https://www.biostars.org/p/308573. A user replied that a de novo assembler such as [SPAdes][1] (which is used in [HybPiper][2]; a pipeline to extract target sequences from ra ...
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Paralog detection after target capture - HybPiper
... We have performed target capture/enrichment for gene regions of interest ([baits][1]) and I am now using [HybPiper][2] in order to extract target sequences from high-throughput DNA sequencing reads. Very briefly, after quality trimming and adapter removal with [Trimmomatic][3], reads will be first ...
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Comment: C: PERL: How I can "save information in a hash (%)"?
... This question is way too vague... I would advise to rephrase it and be more precise on what you really want to do ...
written 23 months ago by Santiago Montero-Mendieta120
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Answer: A: Should replicate analyses of ADMIXTURE all have the same cross-validation values
... I have also noticed identical CV-error values for every replicate ADMIXTURE run. This is due to the initial seed number that is always 43. There is an option of generating a pseudo-random seed using the system clock (flag -s). Here is how I ran it: admixture -s time --cv file.ped K -jN ...
written 2.0 years ago by Santiago Montero-Mendieta120
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Converting a big SNP genotype table to plink (.ped) file for ADMIXTURE
... Dear everyone! I have a big SNP genotype table (about 6 million SNPs) with the following format: SNP_ID ind_1 ind_1 ind_2 ind_2 ind_3 ind_3 snp_1 A A A A G A snp_2 T T T T T T snp_3 ...
perl snp admixture plink ped format written 2.0 years ago by Santiago Montero-Mendieta120 • updated 2.0 years ago by Philipp Bayer6.1k
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Comment: C: Problems creating a blast database
... Olá Lucas, I would recommend you to please make sure you have everything available in your working directory. If you still have problems, you could try to automatically annotate your transcripts by using [autoTrinotate.pl][1] instead. I wrote a tutorial about this some time ago. You can find it her ...
written 2.1 years ago by Santiago Montero-Mendieta120
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Answer: A: Trinotate error DBD::SQLite::db do failed: no such table:
... The TRINOTATE software provides a boilerplate SQLite database that comes pre-populated with a lot of generic data about SwissProt records and Pfam domains. Please make sure that you downloaded the TRINOTATE pre-generated SQLite database and decompress it: wget https://data.broadinstitute.org/Tr ...
written 2.1 years ago by Santiago Montero-Mendieta120
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Answer: A: Problems creating a blast database
... The free version of BLAST2GO can only be run through a graphical interface and is going to take forever on such a big dataset. Nowadays there are better alternatives to functionally annotate a transcriptome. I suggest you trying [TRINOTATE][1] which is very easy to run and it will give you comments ...
written 2.1 years ago by Santiago Montero-Mendieta120

Latest awards to Santiago Montero-Mendieta

Teacher 18 days ago, created an answer with at least 3 up-votes. For A: Prepare gene families for CAFE
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Is TransDecoder predicting the "true" set of protein-coding regions?
Supporter 2.0 years ago, voted at least 25 times.
Scholar 2.1 years ago, created an answer that has been accepted. For A: Trinotate error DBD::SQLite::db do failed: no such table:
Autobiographer 2.8 years ago, has more than 80 characters in the information field of the user's profile.

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