Help with 2nd read data analysis

Question

[jmirobla]

Analysing 2nd read from a V3 run on a HiSeq and I've goot the below image about quality:

Could anyone let me know if it is ok to trim the last 5-10 bases? The data woul still be usefull?

Many thanks

[andrew.j.skelton73]

No Image showing up. I'd advise you check this out, for common explanations around RNA Seq data

[Devon Ryan]

I fixed the image link.

[GenoMax]

Still no go on the image.

[Devon Ryan]

I wonder if every IP gets different hash. The current URL that works for me is http://s9.postimg.org/419yhqedp/2nd_read_quality.png

[GenoMax]

For reference: I am only seeing "enter image description here" in the original post. I can see the image at the link you posted.

[Devon Ryan]

Weird, they're identical links. I suspect that postimg is doing something on the back end to make it hard to directly link an image.

[GenoMax]

Either that or some quirk with Biostars code. I am going to do a test and post the same link here.

Image.

Edit: Does not get inserted into post using the "image" tag but a regular hyperlink works fine.

[Devon Ryan]

Weird, I see the image. When you click on the link, do you go directly to an image or to a webpage?

[GenoMax]

If I click on the link I go directly to the image.
Second line (image word) in my post has the same link with "image" tags and that does not work.
Update: It looked like biostars code had added a "!' before the Image tag. Taking that out made it work.

Answer 1

[Devon Ryan]

Sure, you can do a bit of quality trimming if it helps. The quality isn't really that bad (anything above 5 or so is useful for most things).