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Forum: Oxford Nanopore 06-26-2018, 04:20 AM
Replies: 0
Views: 2,023
Posted By iltisanni
Nanopolish and pilon are calling wrong bases

Hi,

we sequenced and assembled a pichia genome with canu and afterwards polished it with nanopolish and with pilon+illumina reads.

We noticed that the nanopolish Assembly grows against the canu...
Forum: Bioinformatics 05-17-2018, 03:35 AM
Replies: 3
Views: 571
Posted By iltisanni
Still no answer in the community forum but I...

Still no answer in the community forum but I think I found a workaround:


uncollapse all, select all leaves, list summary, copy everything into an editor, delete blank lines and replace : by \t...
Forum: Bioinformatics 05-16-2018, 09:38 PM
Replies: 3
Views: 571
Posted By iltisanni
OK thank you. I will try to find an answer...

OK thank you.

I will try to find an answer there and if I get one I'll post it here aswell.
Forum: Oxford Nanopore 05-16-2018, 05:52 AM
Replies: 15
Views: 8,956
Posted By iltisanni
Have you tried starting the service via terminal...

Have you tried starting the service via terminal manually?
On our Ubuntu 18.04 the minion is not detectable (Unable to connect to the MinKNOW manager instance) until I execute the following...
Forum: Bioinformatics 05-16-2018, 05:12 AM
Replies: 1
Views: 721
Posted By iltisanni
For those of you who are searching for something...

For those of you who are searching for something like me.

http://www.mgc.ac.cn/VFs/main.htm

I think this db is quite helpful and you can download it to yout local drive.
Forum: Oxford Nanopore 05-16-2018, 05:07 AM
Replies: 5
Views: 3,597
Posted By iltisanni
Thumbs up Update: We sequenced some genomes so far...

Update:

We sequenced some genomes so far (rapid sequencing Kit - SQK-RAD004) and the software we are using successfully on Ubuntu 18.04 is:

albacore - for basecalling (of course)
porechop - to...
Forum: Bioinformatics 05-16-2018, 04:59 AM
Replies: 3
Views: 571
Posted By iltisanni
MEGAN - species summary

Hi,

for those who know the free (community) MEGAN software.

We sequenced a metagenome and now want to know what species with how many reads were found overall. If possible in a table like this:...
Forum: Bioinformatics 05-16-2018, 04:51 AM
Replies: 0
Views: 445
Posted By iltisanni
Prokka Annotation - How to use blast nr DB

Hi,

I want to annotate an assembled Pseudomonas Genome (fasta) with prokka.
I was successfull so far but I'm not sure where the information comes from.

I first downloaded a related...
Forum: Bioinformatics 05-14-2018, 04:52 AM
Replies: 6
Views: 1,048
Posted By iltisanni
Oh Hey.. I just recognized the "merge" function...

Oh Hey.. I just recognized the "merge" function which is included with the all option.

I guess this does what I want...I will try it. Alle the other functions coming with the "all" option are not...
Forum: Bioinformatics 05-14-2018, 04:29 AM
Replies: 6
Views: 1,048
Posted By iltisanni
I'm not sure about the "fixstart" option. We want...

I'm not sure about the "fixstart" option. We want exactly what is written for the "minimus2" option but "fixstart" just sets a new starting point at the first dnaA gene if finds. But it does not...
Forum: Bioinformatics 05-14-2018, 12:25 AM
Replies: 6
Views: 1,048
Posted By iltisanni
Thank you. You helped me a lot and your...

Thank you. You helped me a lot and your suggestion to align the sequence against itself was right. Now I found the trimming point and trimmed the fasta with a simple cat X.fasta | cut -c 1-XXX >...
Forum: Bioinformatics 05-11-2018, 04:02 AM
Replies: 6
Views: 1,048
Posted By iltisanni
Nanopore - circular Assembly

Hi,

we succesfully sequenced a DNA sample and assembled the genome with canu.
We got one circular contig which is perfect. But the contig is overlapping.

Since nanopore Reads are very long...
Forum: Bioinformatics 03-19-2018, 06:21 AM
Replies: 0
Views: 559
Posted By iltisanni
SNPs detected in spades Assembly

Hi,

we assembled one 150bp paired-end illumina sample with spades 3.10 and got about 400 contigs with a size of > 1kb.

Afterwards we scanned for SNPs with samtools/varscan with the same...
Forum: Oxford Nanopore 02-05-2018, 12:50 AM
Replies: 5
Views: 3,597
Posted By iltisanni
Thank you. I hope our MinION arrives this...

Thank you.
I hope our MinION arrives this month, then I will use your recommended Software and see if the output satisfies me :-)
Forum: Oxford Nanopore 02-04-2018, 09:12 PM
Replies: 5
Views: 3,597
Posted By iltisanni
That's great. Now how about the further...

That's great.

Now how about the further software pipeline.
Any recommendations for denovo Assembly, Alignment, (differential)gene-expression, snp/indel detection?
Forum: Oxford Nanopore 01-31-2018, 05:23 AM
Replies: 5
Views: 3,597
Posted By iltisanni
Favourite Software

Hello,

within the next months we want to start our own runs with the MinION.
___________________________
One question besides:
First I read that the reads are in hast5 format and have to be...
Forum: Bioinformatics 01-10-2018, 01:58 AM
Replies: 1
Views: 721
Posted By iltisanni
Database for pathogenomics

Hi,

we sequenced some organisms and want to know whether they are human-pathogen (toxic).
Does anyone know if a special database exists where I can scan my assembly scaffolds and check if my...
Forum: General 03-31-2017, 03:00 AM
Replies: 4
Views: 1,391
Posted By iltisanni
Another, but actually the main problem is: ...

Another, but actually the main problem is:

The DNA-Profile of a sample clearly shows that one sample has the alleles 17/19 (capillary electrophoresis) for the marker D22S1045 but NGS only reports...
Forum: General 03-30-2017, 11:50 PM
Replies: 4
Views: 1,391
Posted By iltisanni
I deleted all lines with @ and + and the quality...

I deleted all lines with @ and + and the quality line with sed, reversed the sequences with | rev and created the complementary sequene with sed. (so far nothing wrong?)
Now my grep finds more than...
Forum: General 03-30-2017, 11:00 PM
Replies: 4
Views: 1,391
Posted By iltisanni
Thx for your quick reply :-) 1. Thx. Haven't...

Thx for your quick reply :-)

1. Thx. Haven't tried that so far. I'll try today.
2. Yes... that's what I suggested... I have to speak with our Guy who sets up the FGx
Forum: General 03-30-2017, 04:52 AM
Replies: 4
Views: 1,391
Posted By iltisanni
Question Illumina MiSeqFGx - fastq vs. StrResults.txt

Hey,
I'll write my Bachelor Thesis in a few weeks and I'm new to NGS, so maybe this is quite a noob question -:) however, these ar my problems:
1)
We are sequencing different markers like D3S1358,...
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