Forum: Pacific Biosciences
07-02-2019, 04:56 AM
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Replies: 1
Views: 3,575
Import a BAM file into SMRT Link
Hello everyone,
I just sequenced bacterial genomes by PacBio Sequel. Compared to the RS II technology, I received a BAM file from the sequencing platform. I would like to import my sequencing data...
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Forum: Pacific Biosciences
04-10-2018, 11:49 AM
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Replies: 2
Views: 4,675
Assembly of a mycete genome with HGAP4
Hello,
I need to assemble a fungus genome for which no information is known. When doing the assembly with canu, I get an assembly of 4918 contigs with a total of 57 123 496 bp. However, with...
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Forum: Bioinformatics
08-17-2015, 08:04 AM
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Replies: 1
Views: 591
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Forum: Bioinformatics
08-11-2015, 07:24 AM
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Replies: 1
Views: 591
Own substitution matrix
Hi,
I would like to generate my own substitution matrices (nucleotides and amino acids) using multiple alignments. I'd like your opinion on how to generate these matrices.
Thank you :)
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Forum: Bioinformatics
05-18-2015, 09:57 AM
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Replies: 1
Views: 1,056
tblastn bug?
Hello,
I have a problem with tblastn. I tried to research this protein sequence:
>BN1129_RS00085
MNKVLVAGILGLMLTACGQKEEAAAPAATPAADVAATVEQAASEATSTVEKVASEATATVEKAVSKAEAAVSDAKAN
In the draft...
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Forum: Bioinformatics
05-11-2015, 06:03 PM
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Replies: 2
Views: 2,754
BWA - read identity
Hi,
I'm using BWA to map my short sequencing reads (Illumina MiSeq) on a reference sequence. Is this possible to set the minimum % of identity with BWA? For exemple, if I set 90%, then all reads...
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Forum: General
04-01-2015, 04:07 PM
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Replies: 1
Views: 2,072
too high sequencing coverage
Hi,
I sequenced by Illumina MiSeq some phage genomes. Normally, with bacterial genomes, I have an average sequencing coverage of 75-90x. But with the phages (much more small genomes) the coverages...
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Forum: Bioinformatics
02-08-2015, 04:31 AM
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Replies: 1
Views: 1,028
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Forum: Bioinformatics
12-16-2014, 04:38 AM
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Replies: 4
Views: 1,784
Hello GenoMax,
Thank you for your answer....
Hello GenoMax,
Thank you for your answer. The thread does not really seems helpful for me. I have >1000 sequences in amino acids, is there a way to perform a "blast-like" alignment to get the COG...
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Forum: Bioinformatics
12-15-2014, 03:41 PM
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Replies: 4
Views: 1,784
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Forum: Bioinformatics
12-11-2014, 04:32 PM
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Replies: 4
Views: 1,784
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Forum: General
10-04-2014, 07:39 AM
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Replies: 1
Views: 816
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Forum: Bioinformatics
10-04-2014, 07:31 AM
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Replies: 4
Views: 1,730
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Forum: General
10-04-2014, 07:29 AM
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Replies: 3
Views: 2,423
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Forum: General
10-03-2014, 06:47 PM
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Replies: 1
Views: 1,064
How to correct a ref seq using Illumina
Dears colleagues,
Last year, I made the assembly of a complete bacterial genome using 454 sequencing reads. However, as you probably know, 454 technology is prone to frameshift. Consequently, I...
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Forum: Bioinformatics
08-07-2014, 04:03 PM
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Replies: 1
Views: 1,642
fasta35 VS fasta36
Hello,
I need to use, for a specific job, fasta35 and not fasta36. However, the result is clearly not the same between both.
fasta35 gives only 1 alignment: http://pastebin.com/f4NdYJCt
...
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Forum: Bioinformatics
07-27-2014, 10:05 AM
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Replies: 6
Views: 1,211
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Forum: Bioinformatics
07-26-2014, 05:07 AM
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Replies: 6
Views: 1,211
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Forum: Bioinformatics
07-25-2014, 04:26 PM
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Replies: 6
Views: 1,211
Pairwise alignment from a consensus in query
Hello,
I want to look for a specific gene in a genome sequence. The gene sequence is degenerate and a colleague has suggested that I should make a multiple alignment of orthologous genes, make a...
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Forum: Bioinformatics
07-25-2014, 04:25 PM
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Replies: 1
Views: 1,073
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Forum: General
07-20-2014, 02:51 PM
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Replies: 2
Views: 3,497
% of similarity to be orthologous
Hello,
I have a philosophic question: What is the minimum similarity (% of amino acids) to consider two genes orthologous? Are there some studies about that?
Thank you :)
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Forum: Bioinformatics
03-05-2014, 06:26 PM
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Replies: 3
Views: 1,271
Annotation of a bacterial genome
Hi,
I'm pretty sure that this question was already ask many times but I don't find any post with clear answers. I'm looking for an annotation tool for a bacterial chromosome and plasmids. What is...
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Forum: Bioinformatics
02-12-2014, 04:32 AM
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Replies: 2
Views: 1,588
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Forum: Bioinformatics
02-09-2014, 05:09 PM
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Replies: 2
Views: 1,588
Complete .gbk with Artemis
Hi,
I'm using Artemis for annotated a little genome fragment (50 kb). I can save my sequence in gbk and my ORFs in other gbk file, but is this possible to have a complete .gbk (sequence + ORFs)?
...
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Forum: Bioinformatics
11-13-2013, 05:30 PM
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Replies: 2
Views: 1,149
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