[ASSIGNMENT 1] What detailed instructions do you need

[sr320]

Please list out what detailed intructions you would like ie how to make a blast database.

[JaviRobles]

Hi! I would like to see again, on the screen how did you download the .fasta file from NCBI. -What kind of sequences or data need to include in the file; nucleotide or aminoacids? (I guess both in a separate file), but I would like to follow the process.

After all I guess my doubts could be clear.

FYI. I'm in the other room. :)

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Example is in this notebook and directly via this link

[elizabethbrassea]

Hi! I want to know how to blast a .fasta file thats have information from diverses taxa in the same file with genebank and another plataforms simultaneously

Elizabeth

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Blast would be the same, you just need query and database. I would suggest not combining genbank and other databases. Do one, then another. You could then Join the results (ie SQLShare)

[EugenioCarpizo]

Hola

I need detail instructions to do the blast in yupiter also to merge tables in SQLshare

Eugenio

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Blast example

Merging tables example in this notebook

[carlauranga]

Hello, thank you for this awesome course! :bowtie: I definitely still need help with adding local figures to my Markdown file. Any help with this would be greatly appreciated.

Is there a file for navigating between Jupyter 2 and 3? Some commands from Jupyter 2 are not working with Jupyter 3. Are there advantages to using Jupyter 3 or should I have downloaded Jupiter 2?

More detailed information on how to navigate SQL would be great, i.e. everything Steve did today, how would we do it?

I would love to know if codes are written for actually sequencing proteins from mass spectrometry data..... in order to circumvent the use of expensive software packages. Also, is there a way to detect post-translational modifications in proteins?

[lilopez]

I'd like to make a complete exercise with transcriptomic data. How to clean the data (trimming), how to annotate a novel transcriptome, etc. Maybe, we can work with a file with few sequences.

I have a lot of doubts, cause I don't know where to start.

Laura

[jocisterna]

I would like to see the different blast (n,p,x) with small datasets and the interpretation of results again.

Thanks

[lafarga13]

More than a details instructions on an specific analyses, I will like to see a detail instruction of what is the process we will follow (pipeline) from getting our raw data to SQLshare sharing tables... like raw data, qc analyses of reads, assembly.... and do it maybe with a small file feasible to work with our times... thks

[lacroix54]

Hi, I want to know, where i can search commands or codec to use the server SQLshare ?

Thanks,

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There is not a central list of all commands. Here is what we have compiled

[paolabatta]

Could you explain how to combine tables in SQL again please?

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Added simple merging tables example in this notebook

[Patiiiitoo]

Hi! I would like to know if you have instructions to "debug the state of the repo" in the command line, so I can synchronize my gitHub with the Cloud. Thanks

[mdelrio1]

I would like to know the instructions to prepare a fastaq file to: a) remove with adapters and bar codes. b) obtain a quality report for all reads c) trim low quality reads or read sections d) de novo assemble reads e) change contig names f) obtain reports for hit species after blast. g) report gene ontology at different levels h) count to reads from two (or more) different tissues in order to differentiate gene expression

[Clareliza]

Hola, I need detailed instructions to do blastp, blastn and blastx ( differences). Gracias

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The commands are similar - the main difference is whether your data is nucleotide or protein.

[JVLF]

Hey

I need help with blast comand line.

1) Download (the source did not work) 2) Run in terminal

thanks

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@JVLF What is your operating system?

OS X 10.11.1 (El Capitan)

No worries, Paola shares me the source , thank you!

[astridluna]

Hola

I would like you could repeat please the last part about SQLShare. How can I interpret the colums?

[armandomaxfli]

Hi

I would like see again how download .zip files from database portal, and translate to .fasta file.

Also I would like look others database for proteins or nucleotides for plants or microorganism, for compare to my sequences.

Thanks

[anaidsaf]

Hi I need repeat the exercise transcriptome or proteome data because the web page no connect or error. and then how can I annotate a transcriptome of no model organism.

[MaiderJustel]

I would like to do the comparison of transcriptomes from 2 diferent species and blast in Gitbash /Terminal.

Thanks

[RicardoPJ]

Hi,

Can we see a terminal ( blash) file.csv in ordered columns in the terminal without a graphical interface? And , What command we need?

[DNAlejandro]

Hello. I would like more detailed instructions on today exercises and maybe more clear examples of uses and application of those -particularly for SQLShare-

Thank you very much!

Alex

[Macuarro]

I would like to know: How to extract annotations from a file using SQL

[edlopez78]

I need to do a transcriptome analysis from the begining.

Thanks

[dmartinez4]

I would like to know if there is any way to sync what i have done in the desktop computer and keeping practicing this exercises at home. I would like to know some example of differential gene expression in plants.

[PabloFQ]

Jelow!

Could you explain a little more how works the SQLShare

Thanks

[ROCIOGUERRERO]

Hi!

I would like to know how i can assemble a novel transcriptome?

thanks

[EugenioCarpizo]

I will need more practice with python to get more familiar with the comands

[jazmincastro89]

Hi i have a question about the last part of the blast, how a can compare male and females from the FASTA files (geoduck) D: ? and, i do not understand the command used in the SQLshare :(

Tnks :)