News:Questions for the NCBI Next Generation Sequencing Online Workshop Can be Posted with the NCBI_NOW Tag

Question

[DCGenomics]

Questions for the NCBI Next Generation Sequencing Online Workshop Can be Posted with the NCBI_NOW Tag

[tayyibnaseem]

What will be the timing?

[DCGenomics]

The course will be open through 10/23. During that time, participants will watch six or seven videos (depending on Linux familiarity) and can ask questions here on biostars. There is also a hands on module, to be done in a cloud environment, and questions can be posted here. The videos and hands on module will be publicly available after the 10/23 (there will be a delay of a few weeks for some of the videos), but we will only answer questions directly pertaining to NCBI resources (and they must be sent to [e-mail]. Thanks for your interest!

[mduffourc251]

I have never used Linux. The lecture on Introduction to Linux does not include how to download/access it. Can you provide this remedial information so I can practice the lesson on my own desktop? I run Windows based PC

[cutsort]

Two options for Windows:

1. Codecademy's "Learn the Command Line" (only requires a web browser)
2. Software Carpentry's "The Unix Shell" (which encourages using Git for Windows)

Answer 1

[DCGenomics]

The NCBI Next Generation Sequencing Online Workshop is a very basic online workshop for biologists just getting into next generation sequencing who may want to use NCBI data or tools in that analysis.

A registration link can be found here: https://oraulearning.org/?partition=ncbi

The videos will be released on 10/13/2015, and the hands on portion will be released 10/20/2015.

[ivigoral]

Where can i get information about that course? There is no information about the course on link, you gave

Answer 2

[kazekage.qrq]

Well hello guys. I can't access youtube videos in my country. It is banned here so kindly post the youtube link of posted videos so that I can access them through proxy sites. Thank you.

[Mary]

Oh, that's too bad. Can you see Vimeo? Or SciVee?

Sample Scivee: http://www.scivee.tv/node/46389

Sample Vimeo: https://vimeo.com/42529425

I'm curious too because we use YouTube for videos and I didn't realize this was an issue. And rather than forcing people to use proxy sites, I'd like to know if there's another route.

(I am not answering this for NCBI, this is separate for my own information.)

[kazekage.qrq]

Yes. Thanks Vimeo works fine. The lectures are uploaded there also? If yes that will be good.

[DCGenomics]

The YouTube links will go completely public a couple weeks after the course. Thanks for your interest, and I hope you watch them then!

[Mary]

If you guys could create a Vimeo channel for them too, it would help Kazekage.qrq and others in places that block YouTube.

[kazekage.qrq]

Too bad. I am very eager to learn new stuff from these lectures but have to wait that long. I think the team should setup lectures on another sites like dailymotion, vimeo, etc.

Answer 3

[DCGenomics]

Here's a link to the announcement!

http://www.ncbi.nlm.nih.gov/news/09-30-2015-ncbi-now-next-gen-seq-course/

[Istvan Albert]

I have been watching the course - I think they are too information dense.

I would suggest breaking it into smaller pieces. Also it is not properly clear to me what is your target audience. Teaching bioinformatics, software installation, unix commands, SAM and VCF format bwa, gatk, vcf, fastqc etc just two lectures feels completely overwhelming. Each of these subjects are gigantic on their own.

In addition it skirts around the most important issues of them all. And that is that none of these tools actually works the way someone naively may think so. Aligning two sequences depends solely on the scoring matrix and alignment parameters. Changing those will change the alignments. Those alignment parameters in turn define what type of differences can be found and reported. And are the reason that so many variants cannot be reliably determined.

[DCGenomics]

Thanks for watching! I think you are right. For the next iteration and likely for the public videos we need to split the content and provide links to resources and hands on when possible.

Answer 4

[ayega17]

Hi!

Someone have trouble with quality video?, for example Lecture 2, The FASTQ FILE Forme looks blurred!! Help!

[DCGenomics]

Referred to video editing department.

[wmatten]

About all you can do is be sure you have selected the highest Quality, 720p. If you view at YouTube you have the option for a bigger view without going all the way to full screen.

Answer 5

[hagemani]

I saw the announcement directing participants to carefully read the instructions about applying for Amazon cloud grants---however, it was not clear where these instructions would be located. I am inferring that cloud storage will be needed for the hands-on exercise, and that Amazon will be offering some storage on a limited basis.

[DCGenomics]

Please see comment about wiki below

Answer 6

[Fadel]

Hi all,

Regarding lecture 2 "The FASTQ File Format"

I'm trying to do quality control for raw data for a genomics class, here is the fastqc report for Read1!

my questions are:

in this case should I do trimming or masking?

if trimming, should I trim the position 14-15 and 54-55 ? I could understand the logic behind trimming the 3' end but how I can trim in the middle of the read? Im sorry if my question quite basic but Im really suffering in understanding this concept and if u guys kindly provide me with any reference to read I would highly appreciate ur kindness.

thanks :)

[sijungyun]

Hi, this is Sijung, who did the lecture 2. Unfortunately, I cannot see your html. What I understood is that the quality scores of the position 14-15 and 54-55 are not good enough. In this case, both trimming and masking would work. If you are interested in doing trimming, you may simply want to save column 16 to 53, which could be done in Galaxy (NGS:QC and Manipulation => Trim sequences => 16 for 1st base to keep, and 53 for the last base to keep

You may also trim based on quality - which we often call 'dynamic trimming'. The software program that can do this is FASTX, TRIMMOMATIC, etc.

If it is not still clear, give me an email to [e-mail]

Sijung Yun

[Fadel]

thanks Sijung Yun,

[DCGenomics]

Referred to lecturer for comment.

Answer 7

[DCGenomics]

All instructions for the hands on should be on the wiki page of the github repo.

Please let us know if anything is not clear.

Ben