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Forum: Bioinformatics 04-17-2020, 03:32 AM
Replies: 0
Views: 250
Posted By uloeber
in silico PCR benchmarking

Dear community,
I wonder whether anybody ever did a benchmarking of in silico PCR tools? I couldn't find any benchmarking so far.
Are there any tools you could recommend for command line usage...
Forum: Bioinformatics 01-05-2020, 02:27 AM
Replies: 34
Views: 15,275
Posted By uloeber
Since then there were some SILVA updates, latest...

Since then there were some SILVA updates, latest (V138) end of last year. Would you mind to update the human masked hg19? Much appreciated your effort in the community!
Thank you so much!
Forum: Bioinformatics 01-05-2020, 02:10 AM
Replies: 34
Views: 15,275
Posted By uloeber
how may I create a masked genome reference for mice?

Hi Brian,
I would love to have a masked version of Mus musculus genome. Could you probably share the details how you created the human masked genome, such that I can replicate this for mice?
Bests,...
Forum: Metagenomics 09-10-2019, 04:17 AM
Replies: 4
Views: 3,428
Posted By uloeber
Thank you!

Thank you!
Forum: Metagenomics 09-09-2019, 03:50 AM
Replies: 4
Views: 3,428
Posted By uloeber
Really? I used version 13-5 released this year...

Really? I used version 13-5 released this year 2019-05-01
Forum: Metagenomics 09-03-2019, 02:21 AM
Replies: 0
Views: 1,324
Posted By uloeber
Question Taxonomy tree conflicts in Greengenes V 13.5

Hi all,
I'm using the Lotus pipeline to investigate 16S stool samples. I assigned taxonomy with Greengenes, SILVA, HITdb , since greengenes was updated most recently, SILVA is the biggest database...
Forum: Metagenomics 09-03-2019, 01:52 AM
Replies: 4
Views: 3,428
Posted By uloeber
Question Taxonomy tree conflicts in Greengenes V 13.5

Hi all,
I'm using the Lotus pipeline to investigate 16S stool samples. I assigned taxonomy with Greengenes, SILVA, HITdb , since greengenes was updated most recently, SILVA is the biggest database...
Forum: Bioinformatics 03-07-2019, 03:19 AM
Replies: 252
Views: 103,221
Posted By uloeber
Hi all, What am I doing wrong if I get: ...

Hi all,
What am I doing wrong if I get:

READING READS lib1:
------------------------------------------------------------
Total inserted pairs = 3413702
Number of pairs...
Forum: Bioinformatics 06-01-2018, 02:19 AM
Replies: 131
Views: 66,723
Posted By uloeber
Question Hi Brian, somehow the t=x flag doesn't reduce the...

Hi Brian, somehow the t=x flag doesn't reduce the number of nodes in use. Any suggestions what goes wrong or can I somehow include Java flags?
Bests,
Ulrike
Forum: Bioinformatics 03-21-2018, 05:12 AM
Replies: 1
Views: 1,656
Posted By uloeber
Update

Okay, I gave up on bioperl and wrapped my tabular output.
I got a multidimensional hash structure now.
How may I compare all qstart/qend values of %result{$consensus} and keep only the once which...
Forum: Bioinformatics 03-16-2018, 08:01 AM
Replies: 1
Views: 1,656
Posted By uloeber
Question Parsing Blast xml using Perl (BioPerl)

Hi people,
I'd like to resolve the following problem(s):

I'm trying to resolve the structure of reads, partial of retroviral origin, partial of host genomic origin. In addition, I'd like to...
Forum: Bioinformatics 01-09-2018, 11:24 AM
Replies: 0
Views: 1,551
Posted By uloeber
Haplotype network indels HELP!

Hi all,
I'd like to create a haplotype network including 8 different groups. I have 326 sequences and 84 haplotypes. Some of the haplotypes only differ in indels, but they are real!
I tried R pegas...
Forum: Bioinformatics 07-27-2017, 02:18 AM
Replies: 2
Views: 1,206
Posted By uloeber
Okay, I now might know why bcftools fails (to...

Okay, I now might know why bcftools fails (to many real gaps in long reads which might be sorted out then). Any other suggestions? I do not find an up to date best practice for GATK3/4 or did anyone...
Forum: Bioinformatics 07-23-2017, 04:35 AM
Replies: 2
Views: 1,206
Posted By uloeber
Please help me people, is the question to simple...

Please help me people, is the question to simple or do the 120 readers have no idea as well?
Forum: Bioinformatics 07-20-2017, 03:17 AM
Replies: 2
Views: 1,206
Posted By uloeber
Consensus Calling BCFTOOLS PacBio gaps

Dear community,
I mapped reads from targeted sequencing (PacBio ccs) to a reference (BMA mem - local alignment because I got inverse PCR reads). Most often the complete reference is not covered. I'd...
Forum: Bioinformatics 11-23-2016, 01:03 PM
Replies: 3
Views: 2,532
Posted By uloeber
Hi Brian, Thanks for your reply! I forgot to...

Hi Brian,
Thanks for your reply! I forgot to mention, I want to keep the reads untrimmed. And would your software care about the "both primers present" issue? Otherwise I have again to check every...
Forum: Bioinformatics 11-23-2016, 06:17 AM
Replies: 3
Views: 2,532
Posted By uloeber
Question Demultiplexing PacBio sequences

Hi all,
I have the following problem:
I have a dataset containing circurlarized and linear DNA. It was amplified with two pairs of primers using inverse PCR. I'd like to dissect the data by the...
Forum: Bioinformatics 11-20-2015, 03:31 AM
Replies: 13
Views: 1,657
Posted By uloeber
Why do you think it will work better than...

Why do you think it will work better than TribeMCL? Just giving it a try?
Forum: Bioinformatics 11-20-2015, 03:13 AM
Replies: 13
Views: 1,657
Posted By uloeber
I do not use the full dataset at this step. Yes,...

I do not use the full dataset at this step. Yes, then I have to recover
Forum: Bioinformatics 11-20-2015, 01:43 AM
Replies: 13
Views: 1,657
Posted By uloeber
Question Is it possible to do the clustering with fasta...

Is it possible to do the clustering with fasta files? I lost the quality information a few steps before...
Forum: Bioinformatics 11-19-2015, 09:43 AM
Replies: 13
Views: 1,657
Posted By uloeber
I'll give it a try! bbmap was already so useful...

I'll give it a try! bbmap was already so useful for other tasks. thanks for developing this tool!
Forum: Bioinformatics 11-19-2015, 09:13 AM
Replies: 13
Views: 1,657
Posted By uloeber
@ Brian, they are self-corrected and no, no...

@ Brian,
they are self-corrected and no, no metagenomics, no 16S reads -> inverse PCR reads one organism.

@ GenoMax,
clustal had no problems with the long names. I'm done with everything, the...
Forum: Bioinformatics 11-19-2015, 07:49 AM
Replies: 13
Views: 1,657
Posted By uloeber
Yes, fasta format. It varies from 1500 bp -3000...

Yes, fasta format. It varies from 1500 bp -3000 bp. Two approaches, one: creating a multiple sequence alignment with fixed length, two: taking the longest sequence as seed.
Forum: Bioinformatics 11-19-2015, 06:18 AM
Replies: 13
Views: 1,657
Posted By uloeber
Question PacBio reads: dissect variants by phylogenetic distance

Hi all,
I have the following problem. I have a set of PacBio reads, already filtered and known to cover a specific region of interest.
I'd like to see whether there are clusters of variants in...
Forum: Bioinformatics 10-29-2015, 08:18 AM
Replies: 1
Views: 1,047
Posted By uloeber
Okay, I fixed most of the issues... is anybody...

Okay, I fixed most of the issues... is anybody aware of how to write multiple panels in an output file using
while( my $result = $searchio->next_result )
with
Bio::Graphics::Panel->new
??

I...
Showing results 1 to 25 of 43

 


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