SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 25
Search took 0.01 seconds.
Search: Posts Made By: Morgane_AUS
Forum: Bioinformatics 10-28-2015, 02:32 PM
Replies: 6
Views: 2,473
Posted By Morgane_AUS
Thanks for that ! That's really helpful. I...

Thanks for that ! That's really helpful.

I didn't check which version of Bowtie I was using thinking that the Galaxy main instance would display the most up to date version. I will have a look at...
Forum: Bioinformatics 10-27-2015, 05:26 PM
Replies: 6
Views: 2,473
Posted By Morgane_AUS
Hi, thank you for looking at my data. ...

Hi,

thank you for looking at my data.

I have tried without grooming, just changing data type (my reads are illumina 1.9 encoding) and I have the exact same result.

The illumina fastq...
Forum: Bioinformatics 10-27-2015, 02:30 PM
Replies: 6
Views: 2,473
Posted By Morgane_AUS
See step 14 ...

See step 14

http://galaxy-qld.genome.edu.au/u/m-moreau/h/sample-2-chip-seq
Forum: Bioinformatics 10-26-2015, 04:27 PM
Replies: 6
Views: 2,473
Posted By Morgane_AUS
SAM file after Bowtie is messed up

Hi,



I have chip-seq data from E. coli (51 bp). I mapped my fastq file to my reference genome (custom build) using Bowtie in Galaxy. In the SAM output file, some rows have the sequence in the...
Forum: Bioinformatics 10-25-2015, 07:41 PM
Replies: 3
Views: 1,692
Posted By Morgane_AUS
Hi, did you manage to do what you were...

Hi,

did you manage to do what you were attempting ? Im trying to do the same thing but I'm stuck. Any help would be appreciated.

Morgane
Forum: Illumina/Solexa 12-02-2014, 09:04 PM
Replies: 19
Views: 3,563
Posted By Morgane_AUS
I don't have much DNA in there so I'm worried I...

I don't have much DNA in there so I'm worried I will loose so much by doing it twice... I guess there is no win win situation here ! Finger crossed !
Forum: Illumina/Solexa 12-02-2014, 08:56 PM
Replies: 19
Views: 3,563
Posted By Morgane_AUS
We have the Qsep (similar to bioanalyser) but...

We have the Qsep (similar to bioanalyser) but something went wrong with the cartridge so I had to use a gel. I had to overexpose it in order to see the smear (there is only 1 uL of ladder..).

I...
Forum: Illumina/Solexa 12-02-2014, 08:39 PM
Replies: 19
Views: 3,563
Posted By Morgane_AUS
updated link ...

updated link
https://bioinfo4biologists.wordpress.com/category/lesson-of-the-day/
Forum: Illumina/Solexa 12-02-2014, 08:29 PM
Replies: 19
Views: 3,563
Posted By Morgane_AUS
sorry I don't know what's wrong with the link. ...

sorry I don't know what's wrong with the link.

Here it is. Normal means that ChIPed DNA was used directly as input of the lib prep. WGA means ChIPed DNA was amplified using a whole genome...
Forum: Illumina/Solexa 12-02-2014, 05:36 PM
Replies: 19
Views: 3,563
Posted By Morgane_AUS
I didn't do the two sided size selection because...

I didn't do the two sided size selection because the protocol didn't recommend to do it when starting the lib prep with less than 100 ng (and I started with 0.25 ng !). I'm worried I will loose the...
Forum: Illumina/Solexa 12-02-2014, 04:56 PM
Replies: 19
Views: 3,563
Posted By Morgane_AUS
Mmm.. maybe you're right.. NEBNext ultra DNA...

Mmm.. maybe you're right.. NEBNext ultra DNA adaptor are about 70 bp long (https://www.neb.com/~/media/Catalog/All-Products/33E45F5CD69B497E92C1073F5D551DC7/Datacards%20or%20Manuals/manualE7335.pdf)...
Forum: Illumina/Solexa 12-02-2014, 02:53 PM
Replies: 19
Views: 3,563
Posted By Morgane_AUS
Adapter dimer contamination

Hi,

Have you ever attempted to sequence a library with such a high proportion of adapter dimers ? Please see the gel here:
https://bioinfo4biologists.wordpress.com/category/lesson-of-the-day/
...
Forum: Illumina/Solexa 12-02-2014, 02:44 PM
Replies: 19
Views: 3,563
Posted By Morgane_AUS
How did it go ? :)

How did it go ? :)
Forum: Bioinformatics 10-22-2014, 05:25 PM
Replies: 0
Views: 1,250
Posted By Morgane_AUS
Automated pipeline for de novo Bacterial genome assembly

I found a very easy de novo assembly pipeline for microbial genomes that has been automatised by Andrew Tritt and Aaron Darling from University of California Davis.

See http://wp.me/p58Wz6-1a
Forum: Bioinformatics 09-21-2014, 07:58 PM
Replies: 9
Views: 1,348
Posted By Morgane_AUS
I tried to type <code>mydata </code> but it...

I tried to type <code>mydata </code> but it doesn't work. Also, when I paste some lines from my SAM file, it looses the Tabular format too. Sorry, I'm not sure how to do it. Could you give a bit more...
Forum: Bioinformatics 09-21-2014, 05:27 PM
Replies: 9
Views: 1,348
Posted By Morgane_AUS
How do you paste the data (SAM file) so you are...

How do you paste the data (SAM file) so you are able to scroll to the sides ?
Forum: Bioinformatics 09-18-2014, 10:52 PM
Replies: 9
Views: 1,348
Posted By Morgane_AUS
Yes yes I did, it was set on True. True means...

Yes yes I did, it was set on True. True means Remove duplicates right ?
Forum: Bioinformatics 09-18-2014, 06:03 PM
Replies: 9
Views: 1,348
Posted By Morgane_AUS
duplicate reads still present after MarkDuplicates

Hi,

I removed unmapped reads, I ordered the reads and then I tried to remove duplicates using MarkDuplicates but duplicates are still present (same position, same sequence, the only difference is...
Forum: Bioinformatics 09-17-2014, 10:38 PM
Replies: 1
Views: 1,286
Posted By Morgane_AUS
SNP calling in bacterial genome-worflow

I'm getting confused as to which workflow I should build up to get a list of SNPs I can be confident with. I have WGS data and a custom built reference genome and I'm using Galaxy main for now.
...
Forum: Bioinformatics 09-15-2014, 08:12 PM
Replies: 0
Views: 802
Posted By Morgane_AUS
Newbie question on IGV in Galaxy

In the tutorial I'm following they say:

In the history panel for the newly generated BAM file, click on the ‘display with IGV web current’

I don't have this option in my history.

Is IGV not...
Forum: Bioinformatics 09-02-2014, 06:47 PM
Replies: 2
Views: 1,332
Posted By Morgane_AUS
VarioWatch is for human only, is there a similar...

VarioWatch is for human only, is there a similar program for bacterial genomes ?
Forum: Bioinformatics 08-26-2014, 11:27 PM
Replies: 5
Views: 1,859
Posted By Morgane_AUS
Thanks heaps for your advice

Thanks heaps for your advice
Forum: Bioinformatics 08-25-2014, 03:37 PM
Replies: 5
Views: 1,859
Posted By Morgane_AUS
May I ask what do you use ? Do you do it all on...

May I ask what do you use ? Do you do it all on BaseSpace or do you use a command line program ?

I'm a new bee (as you can guess) and I'd like to know about the other available options and what...
Forum: Bioinformatics 08-25-2014, 03:29 AM
Replies: 5
Views: 1,859
Posted By Morgane_AUS
Yes sorry, I found their support website...

Yes sorry, I found their support website afterwards..

I installed the Bowtie plugin in Geneious and mapped my fastq files to a reference genome.
Forum: Bioinformatics 08-24-2014, 08:53 PM
Replies: 5
Views: 1,859
Posted By Morgane_AUS
Using Geneious to analyse Whole Genome Sequencing data

Hi all,

I'm mapping my reads (obtained from the MiSeq) to a reference genome using the Geneious software. It is a small bacterial genome.

Can anyone explain the following stats ?
...
Showing results 1 to 25 of 25

 


All times are GMT -8. The time now is 04:05 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO