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Search: Posts Made By: SK-N-BE
Forum: Illumina/Solexa 10-14-2018, 09:44 PM
Replies: 2
Views: 531
Posted By SK-N-BE
Thank you for helping me! We use a MiseQ and it...

Thank you for helping me!
We use a MiseQ and it was the first time that we used Nextera Flex instead of XT. And it`s also the first time we got such a string of G.

Beside these issues, I also got...
Forum: Illumina/Solexa 10-12-2018, 01:13 AM
Replies: 2
Views: 531
Posted By SK-N-BE
Do my FASTQC results indicate sequencing bias?

Hello,
I used the Illumina Nextera Flex kit to sequence bacteria (WGS) and I got two warning that I usually do not get when using Nextera XT:

1. overrepresented sequences in the first read (R1)...
Forum: Bioinformatics 09-26-2018, 03:38 AM
Replies: 1
Views: 180
Posted By SK-N-BE
Running qualimap fails:

I tried to run qualimap: http://qualimap.bioinfo.cipf.es/.
When using the command ./qualimap, I am always getting the following error message:

./qualimap Java memory size is set to 1200M...
Forum: Bioinformatics 07-18-2018, 11:11 PM
Replies: 1
Views: 395
Posted By SK-N-BE
FASTQC warnings

I got some warnings in my FASTQC data and I am not sure what these warnings/errors mean.
I sequenced gram positive bacteria (WGS) and got high coverage (more than 150).
Forum: Illumina/Solexa 06-15-2018, 04:27 AM
Replies: 3
Views: 745
Posted By SK-N-BE
Thank you for your answers!

Thank you for your answers!
Forum: Illumina/Solexa 06-12-2018, 10:26 PM
Replies: 3
Views: 745
Posted By SK-N-BE
FastQC warnings

Hello,

using FastQC I always get one error and two warnings for each of my samples (bacterial samples, WGS).

Error:
per base sequence conent
--> here, I assume that tagmentation is the reason...
Forum: Bioinformatics 04-27-2018, 02:37 AM
Replies: 3
Views: 819
Posted By SK-N-BE
Thank you ssbiest. I tried to build my own Kraken...

Thank you ssbiest. I tried to build my own Kraken Acinetobacter database and used a lot of time. However, I was not able. Thus, I have to wait until I have more time to further work on it.
Forum: Bioinformatics 04-17-2018, 05:34 AM
Replies: 3
Views: 819
Posted By SK-N-BE
Here are the 2 remaining files

Here are the 2 remaining files
Forum: Bioinformatics 04-17-2018, 05:28 AM
Replies: 3
Views: 819
Posted By SK-N-BE
Correct species identification impossible?

Hello,

I was using NGS to analyze the phylogenetic relationship of several K.pneumoniae isolates. One of the isolates does not seem to be K.pneumoniae as indicated by analysis of the cgMLST.

In...
Forum: Bioinformatics 04-11-2018, 12:06 AM
Replies: 1
Views: 402
Posted By SK-N-BE
I found the mistake. It was a mistake in the...

I found the mistake. It was a mistake in the command. The following is working:

kraken --db minikraken_20141208 mydata.fasta > sequences.kraken> kraken_mydata.out | kraken-report --db...
Forum: Bioinformatics 04-09-2018, 11:13 PM
Replies: 1
Views: 402
Posted By SK-N-BE
Kraken - why not working anymore

Hello,
until recently, I was only using commercial softwares. Thus, I am new to Ubuntu and command-line tools.

I have installed kraken and last week, I was successfully running kraken. It is...
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