User: Santiago Montero-Mendieta
- Reputation:
- 130
- Status:
- Trusted
- Location:
- Sweden
- Website:
- http://santiagomontero...
- Twitter:
- biomendi
- Scholar ID:
- Google Scholar Page
- Last seen:
- 4 months, 2 weeks ago
- Joined:
- 3 years, 3 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
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... 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 18 months ago by
Santiago Montero-Mendieta • 130
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... 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 18 months ago by
Santiago Montero-Mendieta • 130
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... 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 ...
written 18 months ago by
Santiago Montero-Mendieta • 130
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... 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 ...
written 19 months ago by
Santiago Montero-Mendieta • 130
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... This question is way too vague... I would advise to rephrase it and be more precise on what you really want to do ...
written 2.4 years ago by
Santiago Montero-Mendieta • 130
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... 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 2.4 years ago by
Santiago Montero-Mendieta • 130
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... 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 ...
written 2.5 years ago by
Santiago Montero-Mendieta • 130
• updated
2.5 years ago by
Philipp Bayer ♦ 6.5k
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... 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 2.5 years ago by
Santiago Montero-Mendieta • 130
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... 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 2.6 years ago by
Santiago Montero-Mendieta • 130
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... 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 2.6 years ago by
Santiago Montero-Mendieta • 130
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