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Search: Posts Made By: SK-N-BE
Forum: Bioinformatics 06-12-2019, 01:58 AM
Replies: 1
Views: 2,106
Posted By SK-N-BE
Assembly with trimmed FASTQ files fail

Hello,

spades is working fine when I am using untrimmed fastq files.

I am using Trimmomatic to trim reads (SLIDINGWINDOW:30:20) and used the generated "output_forward_paired.fq.gz" and...
Forum: Illumina/Solexa 02-11-2019, 05:23 AM
Replies: 2
Views: 2,066
Posted By SK-N-BE
Hello, thank you for your reply. I was...

Hello,
thank you for your reply.
I was working with L.monocytogenes and I now found that the Genome size I got is in the range of those genomes that are found on NCBI.
Forum: Illumina/Solexa 02-11-2019, 12:35 AM
Replies: 2
Views: 2,066
Posted By SK-N-BE
Expected genome size vs. assembly total bases

Hello,
I sequenced a bacterial genome with an expected genome size of 2,9 Mbp.
One of my sequenced isolate got 2,98 whereas the second one 3,12 Mbp. Are those results in the range expected? How...
Forum: Illumina/Solexa 10-14-2018, 09:44 PM
Replies: 2
Views: 1,301
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: 1,301
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: 822
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: 801
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: 1,167
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: 1,167
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: 1,213
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: 1,213
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: 1,213
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: 827
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: 827
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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