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Search: Posts Made By: balaena
Forum: Bioinformatics 07-10-2017, 05:39 AM
Replies: 0
Views: 401
Posted By balaena
NCBI genome submission, alternative start codons

Hi,

I wonder if anyone knows how one can tell NCBI submission tools to use alternative start codons for an annotated prokaryote genome.

I used GAG to convert the GFF containing the gene...
Forum: Bioinformatics 06-20-2017, 08:31 AM
Replies: 2
Views: 354
Posted By balaena
this seems to have made it thank you! ...

this seems to have made it

thank you!

now it complains about the cuffdiff output. But I need to have a closer look on that and probably open a different thread if I can't resolve that.
Forum: Bioinformatics 06-20-2017, 06:43 AM
Replies: 2
Views: 354
Posted By balaena
problems installing cummeRbund

Hi

I am having a hard time installing cummeRbund on Ubuntu 14.04. I have upgraded to the latest R version 3.4.0 and tried to install it like so:

source("https://bioconductor.org/biocLite.R")...
Forum: Bioinformatics 02-07-2017, 04:35 AM
Replies: 0
Views: 603
Posted By balaena
Stand-alone KAAS for KEGG annotation

Hi,

I was just trying to use the KEGG tool KAAS on my local computer. But it seems that I don't get all the necessary databases from KEGG without buying a subscription. Is that true? Or do I get...
Forum: Bioinformatics 10-12-2016, 01:31 AM
Replies: 0
Views: 560
Posted By balaena
transcript mapping to non-reference genome

Hi,

I have a de-novo assembled eukaryotic genome and transcriptome. What is the recommended workflow to estimate how many of the assembled transcripts map to the genome?

Thank you!
Forum: Bioinformatics 09-27-2016, 06:38 AM
Replies: 0
Views: 798
Posted By balaena
Sliding window SNP density analysis?

Hi,

is there any tool that can do something like a sliding window SNP density analysis on a vcf file to find genomic regions with a low polymorphism rate? Vcftools can do a consecutive window...
Forum: Bioinformatics 09-13-2016, 04:48 AM
Replies: 0
Views: 828
Posted By balaena
Quantification of shared alleles between two genomes

Hi

I am currently analysing a newly Illumina sequenced invertebrate genome which is highly related to a publicly available reference genome (only trace files available). Both species are thought...
Forum: Bioinformatics 09-13-2016, 02:33 AM
Replies: 1
Views: 1,136
Posted By balaena
Hi, the only one I know is AlignGraph....

Hi,

the only one I know is AlignGraph. Though I don't know if that fulfils your needs.

Best
Forum: Bioinformatics 08-13-2016, 05:42 AM
Replies: 0
Views: 903
Posted By balaena
Low complexity filtering in standalone blastn

Hi

I have difficulties understanding if low-complexity filtering for the query is on by default in standalone blastn.

In the description it says:

-dust <String>
Filter query sequence...
Forum: Bioinformatics 07-29-2016, 05:54 AM
Replies: 0
Views: 833
Posted By balaena
correct syntax for species delimitation in a maf file

Hi,

I want to analyse and manipulate genome alignments with maffilter. So far I have only aligned two de-novo assembled genomes with LAST but as far as I can see, this can only align two genomes...
Forum: Bioinformatics 04-25-2016, 07:43 AM
Replies: 1
Views: 965
Posted By balaena
High amount of low frequency / unique k-mers in Illumina reads

Dear all,

I would like to hear your suggestion what amount of low frequency k-mers in Illumina reads is normal.

I am asking this because I am having a hard time to find a good assembly strategy...
Forum: Bioinformatics 04-04-2016, 09:12 AM
Replies: 46
Views: 21,252
Posted By balaena
40 cores Intel(R) Xeon(R) CPU E7- 8860 @ 2.27GHz...

40 cores Intel(R) Xeon(R) CPU E7- 8860 @ 2.27GHz

1TB Ram

Dataset: 2x 75 million 125bp reads

Thanks!
Forum: Bioinformatics 04-04-2016, 09:03 AM
Replies: 46
Views: 21,252
Posted By balaena
Sorry. No change.

Sorry. No change.
Forum: Bioinformatics 04-04-2016, 08:44 AM
Replies: 46
Views: 21,252
Posted By balaena
Hi Thanks for the suggestion, but it didn't...

Hi

Thanks for the suggestion, but it didn't help. The load goes through the ceiling. I used it like so:

bbnorm.sh -Xmx100g in= in2= out= out2= target=200 mindepth=3 threads=4 pigz=f unpigz=f
...
Forum: Bioinformatics 04-04-2016, 07:43 AM
Replies: 46
Views: 21,252
Posted By balaena
Hi Brian I have difficulties to control the...

Hi Brian

I have difficulties to control the load of bbnorm on our server. Regardless which number I enter for threads=, it will always completely use all idle cores and the load average eventually...
Forum: Illumina/Solexa 11-10-2015, 11:10 PM
Replies: 6
Views: 1,195
Posted By balaena
Need suggestions for Illumina genome sequencing strategy

Hi

I need some advice how to cost efficiently sequence 3-4 invertebrate genomes of around 100Mb. I have some experience from a related genome where we had 2x150bp reads, an insert of 500bp and 80x...
Forum: Bioinformatics 09-21-2015, 01:39 AM
Replies: 7
Views: 3,194
Posted By balaena
Hi Markus thank you very much. Looks quite...

Hi Markus

thank you very much. Looks quite useful. As I understand the output, the results seem to be OK.

- so first column is mode, next column is # mRNAs, then total count of respective...
Forum: Bioinformatics 09-15-2015, 12:39 PM
Replies: 7
Views: 3,194
Posted By balaena
Thanks Markus, I have to check that next week,...

Thanks Markus, I have to check that next week, cause I am away from home on a meeting. I am working with Linux so that is not a problem. Cheers
Forum: Bioinformatics 09-10-2015, 05:52 AM
Replies: 7
Views: 3,194
Posted By balaena
Hi thanks for your reply I'm from Hannover...

Hi

thanks for your reply
I'm from Hannover

below is an example of such a "nasty gene"

actually it is not a nasty gene. It depends on what you define as "exon": only the coding portion or...
Forum: Bioinformatics 09-07-2015, 02:09 AM
Replies: 7
Views: 3,194
Posted By balaena
How to get mean intron, mean gene size etc. from gff

Hi

I have a gff file from a Maker annotation of my genome and I would like to have simple statistics like mean gene size, mean intron etc..

I tried to do it with extraction of the features...
Forum: Bioinformatics 05-20-2015, 08:27 AM
Replies: 0
Views: 648
Posted By balaena
interprete and filter repeatmodeler output

Hi

I have made a repeat-library for my metazoan species genome using repeatmodeler and would like to know how to best proceed with it for gene prediction in maker. Some say to use the...
Forum: Bioinformatics 02-14-2015, 02:21 AM
Replies: 15
Views: 2,770
Posted By balaena
To finalize the whole story, the latest Trinity...

To finalize the whole story, the latest Trinity release (2.0.3) seems to have fixed this problem and the trinity run is also much faster.
Forum: Bioinformatics 02-12-2015, 07:20 AM
Replies: 15
Views: 2,770
Posted By balaena
Seems like this was just the last step. After...

Seems like this was just the last step. After restarting I got the Trinity.fasta.

Thanks!
Forum: Bioinformatics 02-12-2015, 06:40 AM
Replies: 15
Views: 2,770
Posted By balaena
Do you mean restarting Trinity from the same...

Do you mean restarting Trinity from the same location with the previously calculated data still in there?

again with:

nohup Trinity --seqType fq --max_memory 80G --left...
Forum: Bioinformatics 02-12-2015, 06:23 AM
Replies: 15
Views: 2,770
Posted By balaena
OK, I have no storage limitations and there is...

OK, I have no storage limitations and there is plenty of space...

If I execute in the trinity_out_dir (where the .cmds resides):



this happens (last lines of output):
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