SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 12 of 12
Search took 0.00 seconds.
Search: Posts Made By: Jonathan87
Forum: Illumina/Solexa 06-17-2015, 06:17 PM
Replies: 11
Views: 2,197
Posted By Jonathan87
What you refer to as "insert size", to me it's...

What you refer to as "insert size", to me it's the fragment size ... ?
I thought the insert size was the number of bases between the reads. So in your case (fragment size 270, read size 150) the...
Forum: Illumina/Solexa 06-17-2015, 05:34 PM
Replies: 11
Views: 2,197
Posted By Jonathan87
@Brian: Thank you, I didn't know that the std...

@Brian: Thank you, I didn't know that the std deviation of the insert size is so big. If the std dev was lower, assemblers would probably perform better.

@pmiguel I know what 2x75 means, I was...
Forum: Illumina/Solexa 06-16-2015, 09:32 PM
Replies: 11
Views: 2,197
Posted By Jonathan87
But to me a "strong bias toward small insert...

But to me a "strong bias toward small insert sizes" is very different from "The insert size IS 100" ... ? I mean a "strong bias toward small insert sizes" could mean anything. It could mean that the...
Forum: Illumina/Solexa 06-16-2015, 08:07 PM
Replies: 11
Views: 2,197
Posted By Jonathan87
Basic: Why are insert sizes constant?

Hi,

I have a basic question (+ 2 follow up questions) for which there seems to be no answer on the web or I'm applying the wrong search terms ...

1)
I am wondering about why the insert size in...
Forum: General 11-16-2014, 03:15 AM
Replies: 2
Views: 1,408
Posted By Jonathan87
Transcriptome assembly: Why S-shaped length distribution?

Hi,

when you (picture-)google for "transcriptome assembly length distribution" you find distributions that contain a little peak at the end.

For example here:...
Forum: Illumina/Solexa 10-17-2014, 05:00 AM
Replies: 74
Views: 372,250
Posted By Jonathan87
Hi, there are 2 things I don't understand about...

Hi, there are 2 things I don't understand about Illumina sequencing:

1)
What if two reads attach to the flow cell in immediate neighborhood ? I mean when they get bridge-amplified, you will have...
Forum: Bioinformatics 01-02-2014, 11:59 AM
Replies: 5
Views: 3,903
Posted By Jonathan87
Thank you adamdeluca! But seriously, where...

Thank you adamdeluca!

But seriously, where are the instructions ? How can you publish software without giving the slightest hint of how to install it.

Might be obvious for non-newbie linux...
Forum: Bioinformatics 01-02-2014, 11:41 AM
Replies: 5
Views: 3,903
Posted By Jonathan87
BWA aligner: no install instructions ?

I have downloaded bwa and unpacked it via tar xfvj

What do I have to do now?

I see files named COPYING, README.md and NEWS. None of them contains install instructions. There must be...
Forum: Bioinformatics 12-23-2013, 01:52 AM
Replies: 5
Views: 8,364
Posted By Jonathan87
Okay I thought I might understand it on my own by...

Okay I thought I might understand it on my own by asking about this definition but I still don't get it. Actually I'm reading the bowtie manual.
...
Forum: Bioinformatics 12-20-2013, 07:20 AM
Replies: 5
Views: 8,364
Posted By Jonathan87
forward backward strand confusion/basics

Hi,

I was wondering:

which strand do we mean by talking about "THE forward strand"? I mean: if we say "it's the 3'->5' strand" then I would like to know: which one? Actually both strands have a...
Forum: Bioinformatics 01-18-2013, 03:49 AM
Replies: 2
Views: 1,625
Posted By Jonathan87
Because if position i until position i+90 all...

Because if position i until position i+90 all have the same pileup mappability score you do not need to have 90 lines in the file. Instead you record 1 line which indicates the value for each...
Forum: Bioinformatics 01-18-2013, 01:39 AM
Replies: 0
Views: 1,359
Posted By Jonathan87
[Paper] Understanding the mappability-score

Hi forum,

I am reading the paper "Fast Compuation and Applications of Genome Mappability". I'm on page 8 and I'm starting to wonder things:

Question 1

Where do the k-mers come from?

I...
Showing results 1 to 12 of 12

 


All times are GMT -8. The time now is 01:35 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO